I think the OP should distinguish between OMG! optimizing and just ordinary stuff. It's a little weird to see Spellcasting -- an ability that, what half of all classes and prestige classes in D&D have -- put on the same list as Tuaric, Multiheaded, Half-Force Dragons ...
More specifically:
@1 Query whether "most" dungeons are built for medium characters. Many, if not most, monsters are larger than medium size. Certainly many of the iconic ones (e.g., chimeras, beholders, dragons, trolls, giants) are. So, in most cases the monsters are at just as much of a disadvantage as you are.
And, sure, there are some disadvantages to being big, like area effects. But, I think the OP overstates them quite a lot. I don't know how big the map is you play on, but I've rarely found a situation where I can't hit most of the PCs with ye olde Fireball. Whether one of them is big or not has rarely mattered. This is doubly true in a dungeon.
@2 As SorO notes, this is the double-edged sword of Vancian casting. But, it's the case that this weakness of the Vancian casters essentially disappears by about 9th level, maybe before. At that point it's rarely the case that you have so many encounters in a given "day" that you run out of spells, and there are wands, staves, and reserve feats to paper over the weakness.
I will agree that the firepower of casters if often a bit overstated on the boards. There seems to be some slippage between a given build's potential power, i.e., that it can craft an impressive response to any given threat by a given combo of spells, and it's actual, day to day adventuring make up and power. In all fairness, though, the TreantMonk guide to god wizards doesn't suffer from this much.
As a side note, my group is really good about making this a real weakness. We tend to just press on regardless, usually motivated by plot reasons. We've also adopted a slightly more narrative "you are rested and regain your stuff" type of approach, though that's kind of haphazard. We often just do it when we insert the opportunity to level up as well.
As a general rule, I talk about my characters quite a bit with my fellow players and the DM. I try to highlight things that might be annoying, and sometimes potential house rules or nerfs based on those.
EDIT:
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I am inclined to believe most groups that have played together for a good while find a level of power they are all comfortable with.
This has been my experience as well. And, when it hasn't worked it's been b/c the person flat out lied about what he was ok with or not. I'd just want to add that it's a bit more of an art than a science, so some course correction, even within the bounds of a given campaign, should be treated as standard and not as a failing by anyone involved.