TL;DR The simulacrum spell creates game elements that aren't called abilities therefore have no designations. The DM determines how the simulacrum spell's game elements interact with the wider game (see #5).
I've done my best to preserve the words if not the spirit of the original propositions made over the course of the asker's extended argument. If I have misrepresented something, that misrepresentation is accidental not malicious. And if I have rephrased something, that rephrasing was to increase mechanical accuracy or (I hope!) clarity not to dismiss or to obfuscate. Just a head's up: This runs about 2,700 words. Grab a drink.
1. Mostly no
The article does not say to add traits from the construct type to a simulacrum
The Wizards of the Coast Rules of the Game Web column "All About Constructs (Part One)" by Monster Manual author Skip Williams on Artificial Beings, in part, says
An object animated with the animate object spell is a construct. So are most creatures that are built through some artificial means rather than bred, cloned, sprouted, or created through any natural process.
Not all artificial creatures are constructs. Spells such as animate dead and create undead produce undead creatures, not constructs. The simulacrum spell creates a duplicate of some other creature and the duplicate has the same creature type as the original. In general, a construct is a unique kind of creature, not a previously existing creature brought back from death or an attempt to copy another creature. A construct also usually is built up, piece by piece (except in the case of an animated object) from inert materials.
In a paragraph that begins by saying that not all artificial creatures possess the type construct (Monster Manual 307), the article says that a simulacrum's creature type is the same as the original's creature type. The article does not otherwise mention simulacra. (And parts two and three don't mention simulacra at all.) There is also no mention in the article of artificial life generally gaining one or more traits of the construct type—or gaining the construct type proper—due to the creature's status as artificial life. Artificial life includes creatures that possess the construct type, but that's not all that artificial life includes. The article says so. In fairness to the remainder of the proposition, a simulacrum is not an object, a simulacrum is a creature, and the typical simulacrum possesses awareness and perception.
2. Mostly no
The subject of a polymorph spell may retain and may lose some of its extraordinary, supernatural, and spell-like abilities
In context, the alter self spell says
You retain all supernatural and spell-like special attacks and qualities of your normal form, except for those requiring a body part that the new form does not have (such as a mouth for a breath weapon or eyes for a gaze attack). You keep all extraordinary special attacks and qualities derived from class levels (such as a barbarian’s rage ability), but you lose any from your normal form that are not derived from class levels (such as a dragon’s frightful presence ability).
In the first sentence, supernatural and spell-like modify both special attacks and qualities, and special modifies both attacks and qualities. In the second sentence, extraordinary modifies both special attacks and qualities, and special modifies both attacks and qualities. The sentence's adjectives are coordinating with the nouns, not isolating the word qualities. To be extra clear, the first sentence discusses supernatural special attacks, supernatural special qualities, spell-like special attacks, and spell-like special qualities, and the second sentence discusses extraordinary special attacks and extraordinary special qualities.
This is not to say that there's no ambiguity here (cf. here). Yes, instead of writing, "You must wear black shoes and socks," a writer should write, "You must wear black shoes and black socks," if the writer wants the reader to wear black shoes and black socks, but the writer doesn't have to. I mean, if it's a solemn occasion, then the reader can infer that the writer is mandating black socks instead of allowing the reader to wear his snazzy neon unicorn socks.1,2
Inferring from the alter self spell's context is also possible. Reading the boldfaced sentences above as isolating the words qualities from their adjectives means that the reader must bring meaning to the term quality—and the game doesn't define the standalone term quality or use it in any consistent way. Thus, when the spell is used, the game halts until the DM decrees what, in that DM's opinion, constitutes a quality. On the other hand, if read the way that I suggest, the sentences marshal defined game terms, a player can largely adjust his affected PC's character sheet without DM input at all, and play can continue. Legalistically, the sentences can be read as isolating qualities, but, practically, reading them that way creates new problems in sentences that are about solving problems. (By the way, I'd agree totally that qualities is standalone if it were to have come first—for example, "You retain all qualities and supernatural and spell-like special attacks of your normal form…"—, but that's not what it says.)
3. Half no
There are only attack options (né special attacks) and special qualities
The game puts in a creature's stat block pretty much everything mechanical about a creature into the stat block's entries Special Attacks and Special Qualities (see Monster Manual 6) until Complete Psionic (Apr. 2006) when creature stat blocks see the Special Attacks entry replaced by the entry Attack Options.3,4 (All of these, by the way, are under the umbrella of what the game calls special abilities (see PH 80, DMG 289, and MM 315). I'll be using the term special abilities later instead of a more complicated one.)
I can imagine a reader wanting to read the terms special attacks and special qualities as implying that there are nonspecial attacks and nonspecial qualities. That's actually pretty reasonable. However, I would urge that reader revisit #2 (above) and realize that if qualities is not a standalone term then the reader can modify his affected PC according to the alter self spell (and subsequent spells) without knowing a creature's nonspecial qualities at all. In other words, if you agree with #2 then this proposition moot, and if you don't agree with #2, you'll probably think the rest of this answer is nonsense…
4. All yes
A special ability is either a natural ability, an extraordinary ability, a spell-like ability, or a supernatural ability
…Except maybe this part. At least we agree on this. Thank heavens.
5. I'd say no, but another might say yes
I'd not expect a simulacrum's differences from the original to be suppressed in areas of antimagic
Beyond a simulacrum having "only one-half of the real creature’s levels or Hit Dice (and the appropriate hit points, feats, skill ranks, and special abilities for a creature of that level or HD)," the 7th-level Sor/Wiz spell simulacrum [trans] (Player's Handbook 279–80) creates a duplicate that exists under the following game elements:
- "You [the caster] must make a Disguise check when you cast the spell to determine how good the [simulacrum's] likeness is [to the original]. A creature familiar with the original might detect the ruse with a successful Spot check (opposed by the caster’s Disguise check) or a DC 20 Sense Motive check.
- "At all times the simulacrum remains under your [i.e. the caster's] absolute [but nontelepathic] command.
- "A simulacrum has no ability to become more powerful. It cannot increase its level or abilities.
- "If reduced to 0 hit points or otherwise destroyed, it [the simulacrum] reverts to snow and melts instantly into nothingness.
- "A complex process requiring at least 24 hours, 100 gp per hit point, and a fully equipped magical laboratory can repair damage to a simulacrum."
The game doesn't classify these game elements. This is the crux of the argument. There are at least three choices:
The game elements are imposed upon the simulacrum instantaneously by the simulacrum spell. They are not special abilities. They are beyond them but predicated on the simulacrum being a simulacrum. Since the simulacrum spell's game elements are not otherwise addressed by the game, the DM determines how other game elements interact with them.
In this way, a DM could rule (possibly whimsically and in a way that could make me leave that DM's campaign) that one or more of these game elements are suppressed in areas of antimagic. Likewise, a DM could rule that one or more of these game elements are affected by form-changing effects like the polymorph any object spell. It's possible—and totally okay—to agree with the rest of this answer, end up here, and do whatever you want anyway. Just puttin' that out there.
The game elements are part of the simulacrum spell. They are not special abilities. Changing these game elements requires some way (probably original spell research) of changing the simulacrum spell or some way (probably an adventure) of changing the underlying fundamental laws that govern the whole of Simulacrum Club.5
The game elements become one or more of the resultant simulacrum's special abilities. They aren't classified by the simulacrum spell as natural abilities, extraordinary abilities, spell-like abilities, or supernatural abilities, though, so that makes them, by default, natural abilities: "Natural abilities are those not otherwise designated as extraordinary, supernatural, or spell-like" (PH 180). To be clear, natural abilities are unaffected by areas of antimagic, and natural abilities are unmentioned by (therefore, unless the DM rules otherwise, unaffected by and not lost to) the alter self spell, the polymorph spell, the polymorph any object spell, and even the shapechange spell.
Undoubtedly, there are other alternatives, too. Personally, though, I lean toward the last as I've found that the most playable. (I group the simulacrum spell's game elements into one special ability, name the natural ability simulacrum, add that special ability to the simulacrum's Special Qualities entry in its stat block, and call it good enough. That's worked for me, and I've had no complaints, but I've also never had a PC try to remove that special ability—the natural ability simulacrum—from a simulacrum.)
Until writing this answer, though, I hadn't realized there were alternatives to the way I've always done it. I now think that such alternatives are possible—even if I disagree with them, don't like them, and won't be using them.
6. Yes and no
A simulacrum is artificial but not a construct due to the simulacrum spell alone
The game is the authority on simulacra (although the spell that makes them could certainly be more detailed). Also, a simulacrum is artificial. A simulacrum is not necessarily a construct, though, because, as per the article, a simulacrum "has the same creature type as the original."6 For emphasis: A simulacrum does not possess the construct type because it is artificial life. (#1, above, addresses this.) Further, while each creature that possesses the construct type "is an animated object or artificially constructed creature," not all animated objects and artificially constructed creatures must possess the type construct. "Not all artificial creatures are constructs," says the article.
One reader may infer from the description of an unclassified game element that a game element is a special ability, but another reader can disagree
The proposition is this: "Does the spell simulacrum describe the [simulacrum's] inability to gain in power or ability in a way that suggests it [the inability] is not a trait inherent to its [the simulacrum] being a simulacrum?" This is kind of the wrong question. It makes no difference how the simulacrum spell describes the inability to become more powerful; what matters is that the game simply doesn't say what kind of game element that inability to become more powerful is.
Also, traits in this context typically means game elements derived from a creature's race, type, or subtypes (q.v. MM 5 and 296). The simulacrum spell does not say that the spell gives the resultant simulacrum traits (as per #1, above). (If the simulacrum spell did say that it granted traits but nothing else, then those traits would be undesignated special abilities therefore natural abilities; see #5, above.)
8. Mostly yes
A simulacrum's special abilities are determined by modifying the original creature according to the simulacrum spell, but game elements due solely to the simulacrum spell must be further adjudicated by the DM
The argument's proposition is this: "Are the traits (normal or extraordinary) of a simulacrum defined in the description of the spell that created it and the creature type that the simulacrum was duplicated from?" As previously stated, there are no other kinds of special abilities beyond natural abilities, extraordinary abilities, spell-like abilities, and supernatural abilities (see #4, above); there are no normal qualities to contrast with special qualities (see #3, above). And, again, the simulacrum spell itself adds no further traits to the resultant simulacrum (see #1, above).
That said, this proposition leads back to the DM determining what kind of game elements the simulacrum spell creates (see #5). In sum, does the spell create those game elements for the cosmos, or individually for each separate simulacrum? If the latter, then are the game elements special abilities? If they aren't, then the DM rules how the simulacrum spell's game elements interact with other game elements.
"So about the polymorph any object spell…"
To be super-extra clear, a simulacrum doesn't gain extra traits due to the simulacrum spell (see #7); a simulacrum possesses the traits of the original because it's largely a duplicate of the original with the original's type (see #1—and, wow, was that, like, a week ago?). Also, the 8th-level Sor/Wiz spell polymorph any object [trans] (PH 262) inherits many limits from the 4th-level Sor/Wiz spell polymorph [trans] (PH 262) therefore the 2nd-level Sor/Wiz spell alter self [trans] (PH 197), so the polymorph any object spell has very little extra oomph in this particular regard over the lower-level polymorph spell (q.v. here).
With that in mind, whether a simulacrum of a creature can be changed by a polymorph spell et al. into the same or a different creature yet not beholden to the simulacrum spell's game elements depends on the DM's adjudication the simulacrum spell's game elements (as per #5, and I told you it was the crux of the argument).
In my campaigns, were a wizard to cast a polymorph any object spell on a human commoner 1 simulacrum in an effort to change it into a human commoner 1 that's not beholden to the game elements of the simulacrum spell, the polymorph any object spell would fail (as per Spell Failure (PH 171)) because the desired result is impossible: natural abilities are unaffected by the polymorph any object spell (see #5, above). In my campaigns, the polymorph any object spell just can't do that any more than a summon monster spell can crush an orc with an orca. But maybe in yours it can.
1 This inference may not apply in all areas to all solemn occasions. I know. I'm a native Californian.
2 "Hey, in that description, are those socks with snazzy neon unicorns on them, snazzy socks with neon unicorns on them, socks in a snazzy neon with unicorns on them, or socks that have on them unicorns that are both snazzy and neon?" Ask the DM.
3 Complete Psionic also kicks puppies. And hates unicorns.
4 I'll link to the self-congratulatory Web column justifying the new stat block when I can find it.
5 I'm imagining the neutral god of simulacra hatching a plot to change the fundamental laws of simulacra so that simulacra gain souls therefore giving the god more power than any other god due to the god's nigh-infinite horde of mirror mephits. I'd switch to the middle bullet to run that campaign. That sounds pretty spiffy.
6 The simulacrum spell's material components include "some piece of the creature to be duplicated (hair, nail, or the like)." Thus it's technically possible to create a simulacrum that duplicates any creature that the caster can get a piece of—including a creature that possesses the construct type. (I'd still ask the DM before I spent my XP, though.) This doesn't change this answer at all. Even a simulacrum of a construct (therefore possessing the construct type) still must reckon with the game elements due to its creation by the simulacrum spell.
Note: Thank you for posing this question. I hadn't realized before how much of this I'd internalized until I tried to articulate it to someone who viewed it differently. I also appreciate the patience of any reader who made it all the way here.