@JaronK and NinjaRabbit
Here's my response to all that. It's defining "optimization" as, roughly, "choice of feats, magic items, class levels, and so on." It's not, crucially, defining it as "choice of spells." That strikes me as wrong. The most relevant choice the lowly Fighter gets is his choice of feats, that's what the Fighter class in D&D 3.5 does (unfortunately). The most relevant choice a Wizard gets is his spell selection. That's what he does.
It's weird to me that these two scenarios would count as equivalent optimization: (1) a Wizard w/ Spell Focus for all of his feats but brilliant spell selection, say along the lines of TreantMonk's God builds, and (2) a Fighter w/ a Great Cleave. The Wizard in example (1) seems to me to be using a hell of a lot more optimization. It's not optimization at the level of feats, but the spell choices are highly optimized.
Now, I'm not disagreeing that the higher tier classes are generally more flexible -- the Tier system values flexibility highly -- nor am I necessarily disagreeing that at the upper bounds of optimization the higher tier classes can wreak more havoc on a game. It just seems to me that the level of optimization that we take for granted in spell choices, schools to specialize in, and so forth is quite high.
That's really my point. As a corollary, if that level of optimization in spell, etc. choice is quite high, then I don't know what the equivalent level of optimization Paladin or Fighter or Barbarian is. I have a sense, though, that they perform better than they are typically given credit for.
For what it's worth, I saw this in action quite recently. A friend of mine started playing his first D&D wizard, and wanted to play an elemental-themed god type. And, he's still very much learning the ropes both in spell choices and when to cast what spells and that's w/ my help, the guides on this board (thanks again, btw). And, that's the case even though his build was mind-numbingly simple: aside from a handful of feats, I told him to pick whatever prestige class amused him the most and didn't lose caster levels (he ended up w/ Initiate of the Sevenfold Veil) b/c it frankly didn't matter.