I don't really like anything about the PvP.net interface.
It's clunky. Menus are never responsive and always have a 1 second transition period before becoming usable. The Rune/Mastery and Champion screens being the worst offenders.
The Rune screen's book may look cool, but it just slows down the experience. The page flipping isn't necessary, and a toggle would be fine. I'd readily kill a lot of the flashy stuff just to get something that snapped perfectly into play when I wanted it to. I mentioned this someplace else, but static "magical" stone slabs or something, would be nice, if it would remove the need for slow, unresponsive animated pages.
The Champion screens do have a nice "flow" to them when searching, but again, it also feels like it's chugging to complete it's animations. And, the 3D models on Champion descriptions look pretty blurry and gross - sharp 2D art would be fine.
The Mastery just feels like a web page. Actually, it feels a little worse than World of Warcraft's talent calculator. You know, with the click lag and such. Plus, seeing the typing cursor is pretty annoying and only makes it feel like a web site even more.
Most of the PvP.net UIs could just do with a reduction in flashiness, and improvement in how well they all snap into place and how quickly they become usable.
I know I'm not fond of the friend list/chat notifications/invite notifications either, but since it's maintenance, I can't come up with any specifics, so I'll edit those in later.
Also, the PvP.net interface and in-game UI don't have any cohesive style to them. I know that PvP.net is based off of AIR and bloated flash stuff, but I'd just like to point out Guild War's in-game store and in-game UI as things that really worked well together. Or, more close to home, Heroes of Newerth's excellent lobby/options menus. They look good, and even outside of a game, you feel like what you're loading up is a single, strong experience. PvP.net doesn't have a "LoL" feel, it's more like something off or armorgames.com. It would be nice if the UI and PvP.net teams could work together to find an art style that would symbolize the game itself.