I don't disagree with any of the details of your statement, but I'm not sure I agree with the ultimate conclusion. Many of the 3e balance problems were, as you say, build deeply into the system, but many are fundamental design elements -- not just products of the multitude of options. To pick some examples: Cleric and Druid had a bunch of stacking bonus spells that allowed them to outfight Fighters straight out of the PHB. Wizards advanced in number of spells, the level of spells and the effectiveness of spells while scrolls and wands allowed them to bypass most of the limitations of a finite number of spells per day. Save and BAB numbers didn't work well with how multiclassing allowed you to stack level 1 bonuses. Polymorph magic lets PCs use the monster manual as a self-augmentation menu. These are fundamental problems to the system whether or not you add on a couple dozen splat books.
I agree that there's no way to solve these 3.x problems by hunting down unbalanced combos (except maybe by changing polymorph), but I don't see you couldn't create a new 3.x style game that solved them from the beginning. Will there be unbalanced combos after that? Sure, I'm sure there will be. Searching for unbalanced combos is part of what some people enjoy about the game. But I don't need a game that is safe from charop. I just want a game where I can let my less-sophisticated players choose their own powers without generating useless characters. (And frankly, it's not like 4e was all that good about that. You can get some pretty ineffective characters picking powers from PH1.)