Yeah I just noticed the whole transparent-ness this morning when I logged on. It's okay, but my eyes aren't really used to it and it distracts me a bit :p
Edit: I didn't think about what Sapper pointed out. I guess the transparency is helpful like if you're busy checking something in the menu but you have to watch the game as well (towering.) That's one of the main reasons why I use the zoom out option, so I can still watch the bottom half of my screen while I'm using the menu.