Here are some of the biggest differences that I was hung up on when first learning 3rd edition:
1) tactical movement on a grid
2) attacks of opportunity (for nearly everything)
3) feats
4) class "balance"
5) Challenge Rating
6) 0-level spells, cantrips, and ever-present spells
7) prestige classes
8) the d20 DC system for skills (that took away all DM rulings, as everything was codified)
9) character wealth by level baked into the system
The game looked different too. The art style was no longer based in fantasy illustrations, rather than "this is D&D 'dungeon punk' and it can't represent a character from history, fantasy fiction, etc."
I'm not presenting this as a value judgment. I like things about 3.x - the present. But it seems to be that the game forever shifted in 3rd edition. I can't even run the games in the style I used to 20 years ago or play characters the same way. I don't think anyone does in modern D&D.
Anyone else realizing this?