I might as well give my thoughts, since I spend a decent amount of time here, and want the best for the site, not just for me, but for the majority of people.
The lack of info on the new icons. It has been said many times, but it would be helpful, and would avoid unnecessary spam viewing.
Stats should fill up the empty part of the userpages on the left. We had it before, and it just seems like you made it harder for us to scope out members.
I liked the feature where the audio mainpage would play a a featured song. Obviously you could disable the feature from settings, but I do miss it.
The underjudgment system with the new icons doesn't work as well as before. The Classic portal works very well in you can easily see the total number of UJ submissions, and though icons are nice, just take up more space than needed.
The skins are very nice. I love them. I do wish you could either assign certain skins to certain pages eliminating less favourite ones, or even uploading your own personal skins (this is probably a bit too much to ask for tough).
These are off the top of my mind, but believe when say I love the site design, and like the seperate flash portals, BBS stylings, level icons, new user bar at the top, etc...