Third edition was a fine system. At the very least, it gave us a thoughtful and consistent language for describing a fantasy world. Gone were the days of random fiat stats; now our numbers actually came from somewhere, and really meant something. By far, it's the best edition for describing a consistent world that makes sense.
Unfortunately, as with so many things, the math just doesn't hold up on the high end. There were too many avenues of advancement (BAB, ability bonus, enhancement-to-ability bonus, class-based bonus, multiple item-based bonuses). If you get +1 every few levels, and you get those from a wide variety of sources, then the difference between a character with several sources of strong advancement and a character with fewer sources at a reduced rate, quickly grows beyond the scope of the die. After a few levels, it's too easy for some characters to Always Hit or Never Be Hit or Never Have Their Spells Resisted. They really needed tighter control over their math.
This is exactly one of the reasons my system is breaking levels apart
You can still be a wizard a rogue or a druid
But its not on your character sheet class section
Because that doesnt exist anymore
I dont like the idea that class is a tangible thing (feels like that sometimes in d&d) instead of being an abstract concept
Irl, what makes a doctor? Are there clearly defined class levels? Nah. Dont think so.
But 3.x i think gives us a very good window into how to proceed. A good protoype example is explored in some of the ways things can be built that are out lined in the savage species book. But thats really prototypical. Still 3.x gave a lot of good insight into things like that. If everything is gained in piecemeal bits you dont really get classes with this weird escape velocity acheiving climb to end up in orbit. I think granularity really tamps down on this effect where some classes just have a capacity to raid the pantry so quick. 3.x had some of that but it also had things like the following:
Little bit of dragon wrought kobold here
Be chosen of mystra for a little while
A little psion there
Ooo lets take a little cleric here
Red wizard of thay for 10 levels
Paladin just long enough to get leadership (or even acquire the feat somehow without using a class directly)
Hey dm, im gonna pick a fight with father limmick because his name bothers me like the word moist does