I'll just come out and say it:
 

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.

http://beta.leagueoflegends.com/boar...read.php?t=727

Look at this thread. Things are going to change, hopefully to something like Mardukes exceptional example. We all think its clunky but I'm sure these guys will fix it up for us, they're far and beyond the most in-touch with the community they cater to.

In the current patch you are playing is the patch where we did implement markduke's example (currently partially unskinned, but the same functionality). We will be continuing to add stuff from that thread over the next couple patches as well.

I did hear Lima or hohums say that they are going to add a full frame option that is going to make it even more like Marduke's example.

Yup!

I do see that the friends list got a revamp in recent patches (I've only been in the beta for a short time, so I haven't been able to see progression for myself), but my real worry is PvP.net's menu performance on the whole, which I hope will be addressed.