The small improvement in AC of a tower shield over a heavy shield is not worth the attack penalty or armor check penalty that comes with it.
Everyone who ever wants to make an attack or use a skill that takes a check penalty should not even consider a tower shield, as it will make them suck at doing those things.
The small improvement in AC of a tower shield over a heavy shield is not worth a feat.
Even if you don’t make attacks or use those skills, you need proficiency if you are going to use a tower shield, since without proficiency you take −10 to a ton of rolls, most importantly initiative. All four of the classes with native proficiency are going to want to attack (see 1.), so that means spending a feat.
The cover thing is extremely niche, and if you follow the FAQ, pretty much worthless (the FAQ adds a standard-action cost to gaining cover).
Even ignoring the FAQ, it still isn’t worth a feat (Combat Expertise would be much better), and on top of that, the hide shield from Sandstorm also allows you to get cover, but has way less penalties and does not require extra-special proficiency.
As a result...
There is no situation in which a tower shield improves your character
The key here is opportunity costs. If you are using a tower shield, that means you had to get proficiency in it, acquire a tower shield, and then strap it to your arm. These are not things you can do on a whim, they all have costs. This means that you cannot discuss a tower shield in a vacuum: even if you come up with a hypothetical situation where a tower shield might arguably be useful, you also have to explain how its arguable utility in that situation also justifies all the preparation that using a tower shield requires, and is superior to other options you could have prepared instead of preparing to use a tower shield.
Proficiency is a big issue. Almost everyone has to spend a feat on it. There are exactly four classes that receive proficiency in tower shields (bone knight, fighter, Great Rift deep defender, and warpriest), three are prestige classes, and two of those prestige classes are awful. And the fighter has a fair few alternate class feature options to get things instead of the tower shield (and almost all of them are better). So unless you’re a bone knight, you really shouldn’t be proficient in a tower shield. Even as a bone knight (or, if you really insist, a deep defender or warpriest), it would be massively preferable to steal a figther ACF that replaces tower shield proficiency, if your DM would let you.
So from the get-go, using a tower shield means doing something to get proficiency when you almost-certainly had a better option for the resource used to get it.
But you do have to get proficiency. Because if you don’t, you take a −10 penalty on all Strength- and Dexterity-based ability and skill checks. For anyone thinking that they don’t sneak or jump and thus don’t care, consider that this includes Initiative checks. Using a tower shield you aren’t proficient in means you will go last in damn near every combat you ever take part in. In a game where “going first” is probably the single greatest advantage you can have (and at high levels of optimization, is very nearly synonymous with “winning.”). So using a tower shield requires proficiency.
Keeping all this in mind, a quick run-down of why no one wants to use this thing:
Anyone who wants to make an attack roll will never want to use a tower shield. That includes all four classes that get free proficiency. The −2 penalty on attack rolls is quite bad for such characters, and very-certainly not worth it for a mere +2 AC over simply using a heavy shield. That’s not even getting into the inherent superiority of two-handed weapons over using a shield at all.
And when you could get another feat instead, this stops even being a discussion.
You can argue that in some niche cases, more AC is worth it. These get increasingly convoluted to try and argue that the tower shield is appropriate, but ultimately the real problem is you cannot just apply a tower shield on a whim. A tower shield is not Combat Expertise; that feat lets you trade attack for AC (real AC, not just armored AC) whenever you want to. Rarely worthwhile, definitely not worth a feat on its own, but if you have it you might use it occasionally. Tower shields are like that, except they are only armored AC and you need to buy one, carry it around with you, and then you need to put it on. These are major drawbacks.
And once you get above the lowest levels, the need for magic shields means that switching to a back-up shield costs that much more. A +1 heavy shield has an AC of +3, so your −2 attack for a tower shield is only buying you +1 AC unless you pay more for a +1 tower shield – and tower shield uses are too niche to start investing like that. A +2 heavy shield is as good as a tower shield, but of course you shouldn’t actually buy a +2 heavy shield – you should buy a +2-equivalent heavy shield that has other properties more valuable than AC. Your tower shield isn’t going to have those.
So the only real argument here is a low-level fighter who lacks access to supplements that let them trade away tower shield proficiency. But even then, armored AC is of very low utility relative to attack: the best defense in 3.5 is often a strong offense to begin with, but more importantly, armored AC is just a really limited type of defense. Far too many things outright ignore it – things that are often nastier than the things that don’t ignore it. Carrying around a tower shield for the very few cases where it might be a good idea, assuming you have time to dig it out and equip it, is just wasteful.
You cannot use a tower shield at all while attacking with the overwhelming majority of ranged weapons, so this is even worse than it is for melees. For those exceptions, the tower shield is still just as bad as it is for melee, but ranged characters put even less value on AC.
Even when proficient, the −10 Armor Check Penalty puts a lot of skills in the “don’t even bother” range.
And you have to pay a feat for the privilege.
The tower shield is a complete non-starter for any arcane spellcasters, since it has a whopping 50% Arcane Spell Failure rate. No class or feat in the game, to my knowledge, can eliminate that (as many classes do for light armor, and a few do for medium or heavy armor).
Non-arcane magical types
Divine spellcasters, psionic manifesters, pact-binders, and so on, all have access to effects that do not require attack rolls, and do not suffer from Arcane Spell Failure. In all cases, though, attack-roll based options are often very good, so giving them up is painful – but you can argue that +2 to AC is worth −2 to attacks when you’re making touch attacks anyway. But these classes also tend to have a lot of ability to wade into actual melee, which stops being an option after you strap on a tower shield, and that sucks. Limiting yourself is not worth +2 to AC.
And that’s ignoring the proficiency issue. As soon as we stop doing that, and the option of using a tower shield requires spending a feat or a level, you can no longer even argue in its favor. Bone knights advance cleric spellcasting, but imperfectly – the only reason to become a bone knight is if you’re willing to trade some spellcasting for martial prowess, which means you’re not going to want to degrade your attack and damage to use a tower shield.
About that cover thing
For one, the FAQ claims that gaining cover from a tower shield is a standard action. It outright admits that this isn’t actually in the rules, but claims it is what the rules “meant.” This is basically garbage (the FAQ doesn’t have the authority to change the rules like that); see here for more on why the FAQ is problematic. But if gaining cover from a tower shield costs a standard action, its usefulness is nearly nil: there are really very few situations where that is going to save you when you can’t do much of anything else. It may be something of an option if you get mobbed while your teammates are ignored, but vastly superior panic buttons exist in 3.5 that will do this much better (including a literal panic button magic item!). Turtling is almost never an effective tactic.
If we ignore the FAQ, in theory a spellcaster or something could get decent use from the cover while casting spells. This seems unreasonable to me (spellcasters are already better at everything, why would they be better at something as physical as a giant shield?), and that’s probably why the FAQ makes the claims that it does, but at least this sounds decent.
Except that you still need proficiency. The large penalties you take just to have this as an option are just not worth it for something that so rarely works. Combat Expertise is a weak feat for the same reasons, but it’s still massively better than Tower Shield Proficiency. At least that also improves AC vs. touch attacks, and serves as an important requirement for some pretty good feats. A feat is way, way better spent on Combat Expertise then Tower Shield Proficiency.
Finally, even if we wanted to stipulate that having easy access to cover is valuable enough to have the shield around just for that utility, maybe a cheap mundane one that you don’t use in combat or something, the hide shield from Sandstorm has the same feature, and is vastly less terrible: its ACP is only −3, and you do not need extra-special proficiency in it. Seriously, even if you were kind of thinking that a tower shield has some niche purpose, whatever that niche purpose was is filled far better by a hide shield than a tower shield.
The only semi-useful things about this rely on the fact that it is worded terribly and so some abuses are available that do fairly useful, albeit nonsensical, things. For example, strict-RAW a tower shield can be hidden behind, hiding the tower shield itself. It also, because of the really weird way in which they chose to word things, blocks the Mindsight feat. Neither of these abuses, however, justify the penalties that you take for using a tower shield—if nothing else, you can always just use a hide shield.