Some of the things we've noticed the absence of...
1. Attacks of Opportunity. Not sure yet if I miss them.
2. Listen checks. I liked the die rolling but to be honest, it never made sense as a skill. Now, if there's something that's trying not to be heard, it becomes a Wis v Dex contest.
3. Flanking. I miss it. Playing the rogue put the spotlight on how much I liked flanking. During playtesting, I found that I spent a lot of rounds hiding and trying to get into position for a sneak attack. Meanwhile the wizard and cleric were machine gunning their magic missiles and radiant lances. *sigh*
4. Flat footed. Without it, having surprise doesn't feel all that special. (Edit #1)
5. Touch attack. Miss this one. It makes sense but it requires things like AC vs different things. (Edit #2)