[This answer takes the three separate questions found in the querent's post and numbers them, answering them in numerical order.]
1.) Can spell storing effectively change a spell's target entry?
"Any time the weapon strikes a creature and the creature takes damage from it, the weapon can immediately cast the spell on that creature as a free action if the wielder desires."
While the above statement is somewhat imperfect, it seems reasonable and rational that the exception(s) noted in that sentence acknowledge that they are
(1) granting the weapon the ability to cast a spell,
(2) the ability to cast the spell faster than normal, and
(3) the ability to cast the spell on the creature just struck by the weapon.
The parenthetical aside that follows the above statement only concerns itself with clarifying point (2) - and if the authors wished to be more precise regarding the "allowability" of certain spells or targets ("Can I hit myself with the Mace of Spell Storing of Alter-Self and have it work?"1) then it seems they would have placed such a restriction in that clarifying aside. Lacking such text, it seems the choice to allow spells which target the self to be cast into a weapon of spell storing, and thus to allow such a weapon to change the targets of such spells, to be a deliberate choice.
2.) When the spell that's stored has a target entry of youa is the spell still cast on the struck creature and the struck creature affected by the spell as if the struck creature were youb?
Yes, even if the youa and the youb are completely different people. Given the following line from spell storing:
"Once the spell has been cast from the weapon, a spellcaster can cast any other targeted spell of up to 3rd level into it."
Paired with this one:
"[...] the weapon can immediately cast the spell on that creature as a free action if the wielder desires."
Even if Robert the Sorcerer were the caster and Gerold the Fighter the wielder, despite the line "target: you" referring to Robert the Sorcerer when he casts Alter Self into the Mace of Spell Storing and the "youb" in your statement being the wielder, Gerold the Figher in this example, the party struck by the weapon is still treated as "you," for the purpose of the spell casting from the weapon.
3.) If so, does the weapon's wielder or the subject make relevant decisions about the spell's effect?
It is unclear whether the original spellcaster or the weapon gets to make those relevant choices. The spell storing text reads, in part "[...]the weapon can immediately cast the spell [...]" while it also reads "a spellcaster can cast any other targeted spell of up to 3rd level into it."
This is further complicated by the initial line in the weapon special property being: "A spell storing weapon allows a spellcaster to store a single targeted spell [...]"
Does this mean the weapon stores the exact spell the spellcaster envisions (such as an alter self that changes the target into an elf - which of course would fail to cast if the Mace were to hit a bugbear) or does it mean that the spellcaster stores an "unfinished"2 spell, and when the weapon casts it, then the caster gets to make the relevant choices regarding the spell (such as getting to choose how a levitate spell specifically moves its target) or does it mean that caster places the spell into the weapon, and then if there are any meaningful choices to be made, a non-intelligent weapon makes those choices?
Spells with "effects" have to have relevant choices made during casting (PHB p.175-176), but spells which lack an effect line but can have variable effects (such as levitate or alter self) usually have the caster make those relevant choices only after the spell has been cast. In this case, determining the caster seems difficult, and the rules found within spell storing are unsatisfactory.
A non-intelligent magic weapon is not able to make choices. But then, a spellcaster who is not present for his spell is not able to make good choices.
While it might seem unlikely or illogical that the core rules would include such a bizarre, "two-caster" methodology for a magic iem, it is not the only example of such a method. Merely four pages later, the DMG gives us the rules for potions:
"Potions are like spells cast upon the imbiber. The character taking the potion doesn’t get to make any decisions about the effect—the caster who brewed the potion has already done so. For example, a potion of protection from energyis always designed to protect against a specific energy type chosen by the creator, not the drinker. The drinker of a potion is both the effective target and the caster of the effect (though the potion indicates the caster level, the drinker still controls the effect, such as with levitate)." [DMG p.229]
This offers nothing to help solve the dilemma, but it does support my position that the game designers were conceptually on board with a spell having multiple casters - at least in the cases in which those spells come from items. However, that still leaves the third question unanswerable, or at least, unanswerable in a consistent and rational way. This also supports the answer to the first question, in that this rules-based example clearly shows us a spell's target being legally altered via magical items.
In the end, this DM would likely houserule that the wielder must make those choices, despite such a ruling not fully encompassing the potential complexity and enjoyability the original (though non-sensical) text offered.
1: Of course, such a Mace of Spell Storing of Alter-Self wielder likely does not need the magical weapon property or the spell of the mace, if they are willing to club themselves in the face strong enough, the self with be altered.
2: The term "unfinished" is woefully inadequate for this conversation, but this respondent felt that writing down "a spell which has been cast but whose variable-yet-determinable effects have yet to be determined"
was a bit over wrought.