I want to point out the hilarious contradiction that arose when you said "Other than the one entire branch of spells, another similar but different branch of spells, another group of power, powerful PrCs, and a bunch of other spells, the Wizard's not powerful at all!" Look, it's okay if you like that power level. Just aknowledge that it is powerful.
'Buff stacking' is not the same as the transmutation school. Pulling together 15 different bonus types from 15 different books is not the same as casting Bull's Strength and then Bear's Endurance.
Body of the Wolf and Trollform are not broken. Polymorph is, as it allows dumpster diving.
Things that allow free persistent spell remove one of the few balancing factors to spells. The difference between a wizard or cleric using those feats/classes and a wizard or cleric not using those feats/classes is colossal.
Nodes are broken, pun pun level of broken, that is all.
Shivering Touch and a few other offenders are save or dies without the save. That is again, bad design that doesn't prove the rule. There are few spells like this, and they can be and are spot-banned.
As to your d) point: why should the wizard (or other caster, but this mostly pertains to the Wizard) be as powerful as any other class at what they do? As it is now, wizards are capable of taking care of any situation with no trouble whatsoever. If that's the goal for non-wizards, powerwise, wizards will STILL be the most powerful class by far, because not only are they capable of replacing, say, the Rogue for skill use, but the Cleric for healing/buffing, the Fighter for combat, the Monk for whatever it is the MOnk does, etc. all at the same time. So they are as powerful as any one class at a task as that class is, but have the advantage of being able to do other things (as well as the classes that specialize in those things even).
My point was that wizards and clerics and archivists and sorcerers and erudites
shouldn't be as powerful as other classes at that other class's major schtick. You're assuming that the only way to do this is to nerf wizards. My entire post was stating that I disagreed with that. Did you even read what I wrote?
In Tome, for example, the Wizard can't replace the Fighter. That's because the Fighter can do things the Wizard can't. If the wizard fills all his spell slots and dumpster dives for stupid spells, he can possibly equal the fighter, although some capabilities he can't (BAB scaling feats). I honestly think the Fighter is one of the less well designed and weaker Tome classes.
If you think a wizard can solo any encounter a fighter can survive, you're right, they can. But if the Fighter is stronger, then the encounters that he can survive/defeat get stronger, too. Then it's not that the wizard can solo everything, but rather, that he is on an even footing with the improved fighter, and probably even weaker in combat (utility in lots of situations vs being really good at fighting -> the ideal difference between the fighter and the wizard). That's my argument for creating classes that are actually good at their roles instead of turning the wizard into a magic missile spammer and making the fights all boring hp-slogs, since that's all the PHB melee classes can actually handle without insane optimization.
As to your other points: that's the problem with the casters. Unless you do fix the problems with overly powrful spells, they do indeed do those things. No two ways about it. So by default, they do definitely need to be nerfed....unless you want those points to still be a problem. If you don't care, and want to bring everyone else up to that level, more power to you I guess. But you can't argue that the casters are not the problem and then come around and say "they do have these things that make them overly powerful, but those don't count".
Other than the things I listed, all of which are things I have seen houserules limiting or abolishing in nearly any game of 3.5 i've ever played, there is nothing that the wizard can do that is 'overly powerful'.
Again, the problem is that when compared to stock MM1 enemies, the fighter, rogue, barbarian etc don't stand up very well, and certain other classes have lopsided power flow in terms of what abilities they're supposed to use and what they use (bard = dragonfire inspiration, spells, maybe some skill use for funsies, nothing else, no partial melee without sublime chord buffs, no other bardic music (countersong?) etc etc all that stuff is weak and is ignored) (druids = wildshape, pocket fighter (animal companion), handful of 'good' spells, no skill use or wild empathy or whatever, no-one cares about any of that).
You can nerf wizards and sorcs and clerics and anything else with a spell progression (and all the attempts to nerf spellcasters have been hilariously hamfisted and generally failed (pathfinder, numerous 'fixes' like 'one less glitterdust per day' which just shortens the adventuring day by 1 encounter)) but then the entire party is going to need optimizing to stand up to unoptimized encounters and combat is going to be boring (just like 4e).
I'd prefer to actually make the currently weak and boring melee classes have interesting and thematic abilities that make them good at what they do.
As for the Tome series, my memory of them isn't too hot, as it was a long time ago that I read them, but I remember a distinct design philosophy difference between me and Frank and K. The way they designed things was not the way I prefer to design things, and it did indeed lead to a massive power creep for the mundanes. They made everyone tier 2, when I prefer lower tier 3, as it's much easier to balance, much easier to challenge, and much more efficient at not breaking things. As for feats, they have a bunch grant benefits at higher HD, effectively granting 3 feats for the price of 1. I really do not like this. I prefer more feats being granted, and each feat being useful at all levels.
The idea of those feats was that they were useful at all levels.. granting small abilities at lower levels and bigger/broader abilities at higher levels, like a feat chain without requiring additional feat expenditure. If you want to customize it more, you could change each rank of the feat into a new feat as part of a chain and hand out more feats. That's a personal preference thing, though, most people like the differentiation the feats provide 'my samurai has trained to fight in absolute darkness' etc as opposed to people cherrypicking the strongest feats out of the lot like in basic 3.5.
I'm not Tomesfan9999 but like I said of all the fixes i've seen, it's the only one to create relative power parity between the classes. It's also the only one that has created classes and parties that pass the SGT (Same Game Test) i.e. that can handle the CR of stock encounters they're supposed to handle, without optimization.
For rebalancing attempts that don't just add numbers: me and EjoThims have a Monk, and Ejo's got a Fighter, Barbarian, Rogue, etc. in Verold. For rebalancing attempts on casters: I know Bauglir's been working on an interesting one, that one promises to be good. RobbyPants as well.
Do you have links for these? I could possibly find them with the search function but I don't feel like trawling through it right now.