It's amazing that 3.0 seemed to incorporate so many of our local "house rules" like eliminating level limits, and letting any race being any class, as well as bringing back assassins and monks, we even had a house rule that let characters improve their ability scores as they levelled up. We even had a system for using the character-points from Skills & Powers to buy NWP's as well as special abilities like letting characters use their dexterity on to-hit rolls with light weapons, letting mages have their spells do subdual damage (or not have V, S, or M components), and other abilities, in other words, feats. 3e was taking all our house rules for 2e (which we needed to make it playable really), and remounting them on a consistent, easy to use framework.
3e also solved one of the biggest problems 2e was having towards the end, "legacy code" and rules-bloat. Countless systems in different books for different things (different martial arts rules in Complete Fighter's Handbook, Complete Priest's Handbook, Combat & Tactics, Oriental Adventures & I think also in Complete Gladiator's Handbook), and references to rulebooks you'd need to use a new book, rulebooks that had been out of print for years and never had a big print run to begin with. As well as a gordian knot of rulings, errata, precedent, subtle changes different printings of books, and utterly incompatible or broken suppliments.