My first gut reaction to the original post. Is that D&D 3.0 & 3.5 was just as convoluted and complex. Its the fact that he changed players from a more old school GM centric anything goes to make the story work to players the want to be hold tighter to rules. And that's probably what happened.
I peaked in on the WotC character optimization boards and they certainly did pull liberally from each and every source possible. And from Living Greyhawk/(not coming up with the Eberron campaign name) experience, I saw plenty of character with half a dozen classes each from a half dozen source book. With that in mind, Paizo's Pathfinder has done an awful lot to make it easier and occur earlier.
First and foremost, Pathfinder is far more open with content. With the minor exception of setting based rules, all of Paizo rule base content is open access. This wasn't true for WotC, as the vast majority of their content outside the core 3 books was not open. So it was more difficult to find and use. This has lead to far more adoption of rules from outside the core rules set in Pathfinder.
Second, the rules come in much earlier. In Pathfinder you are making racial substitutions, archetype substitutions, trait selections, and feat selection all at character creation. In 3.x with the exception of feats, all great deal of customization came from prestige classes. Which generally required more time and effort to gain entry into. That said I can't say how much more I prefer Pathfinders archetypes and substitutions producing different characters from the start and not being tied to being quite as front loaded as the 'good' 3.x prestige classes were.