I don't agree with you on this one. I would say that the closest system to 3e D&D is RC D&D. Sure, WoTC separated races from classes in 3e, but the RC general skills -- including the level progression for receiving them -- are very similar to feats. The mechanics for some, like acrobatics, were copied over as 3e skillsThe RC versions of paladins, avengers, and druids could have been the impetus for prestige classes, and the mystic was a base class. The RC wrestling rules are very obviously the ancestor of 3e grappling rules, much more so than the AD&D rules are, and the disarming and hooking (tripping) rules are relatively similar as well. Even the RC combat rules played a major role in what 3e combat became and included rudimentary 5' steps, and the uniform ability score adjustments of 3e also come from basic.
I would argue that 3e D&D is basically Mentzer D&D at its core with some add ons from 2nd ed. AD&D, such as two-axis alignment, races like gnome, half-orc, and half-elf, and classes like the bard and barbarian.