Along with Trampier/Otus/Dee, Specialty Priests, and various others already mentioned, I have a few things I miss:
- XP progression tables that weren't based on 13.333333 encounters to gain a level. I liked the rapid early progression followed by a settling in as players focused on campaign activities rather than power-ups.
- Multi-function spells. 3.5 especially has broken up all of the spells that did different things.
- Character Death as game balance.
- All the little tables in the DMG. That was a book for someone trying to run a campaign. Instead of hand-holding through the basics you got information you could actually use to add flavour and substance to your game.
- Treasure type has already been mentioned, but I think it bears repeating. This is another area where simpler isn't always better. I think they oversimplified monster treasure allocation where they didn't need to. We may not have needed the same range of types, but we sure need more than we've got.
Overall I'm happier with this edition, but I definitely miss some stuff.