Well, I like the feats, skills (though it makes creating NPCs an absolute nightmare in this edition - the skill points quadruple the time it takes to stat an NPC, and even more if the NPC is multiclass), multiclass rules, critical hit rules, more intuitive saving throws, cleric spontaneous casting, prestige classes (well, the concept at least), and better-statted monsters.
I miss the superior monster descriptions (habitat, ecology), specialty priests, race/class restrictions, surprise rolls, and weapon speed factors. [However, I've easily re-introduced all of these except the surprise roll into my 3e game with no detrimental effects.]
For modern/futuristic settings, I prefer FUZION's skill-system as well as its auto-fire rules. I'll stick with FUZION for any futuristic campaign.