My biggest complains are. (biggest complaints first)
1. No way (that I have found) to make the home screen be the "activity from subscriptions" or "subscription uploads only" screen
2. The default screen is sorted by "most likely to watch" instead of by upload/comment made/playlist created time, and no way to change it to that. (Thankfully, the subscriptions pages still sort by most recent thing first) EDIT: Oh, and the "most likely to watch" seems to include lots of suggestions I would never consider watching...
3. Left aligned with no option to change it
4. The "other videos by this person/in this playlist" thing is really small
However, once I am watching the videos or commenting on them, I don't really mind that part of the design at all.