Well. This will take some getting used to, though I'm liking it overall. Considering how huge the change is, the fact that my first reaction isn't "they changed it, now it sucks" is actually rather more positive than it sounds... it is easy to grow comfortable with something and start hating when it's taken away

I do have some feedback though.
Elite theme
1) The transparency seems a bit on the high side, and can distract from the actual text. The visual effect is nice, but it could stand to be toned down just a little.
2) I would prefer if the thread page navigation and forum quick navigation were buttons you could click to pop up the menu rather than a mouse-over function. They tend to pop up when I don't want them to while I writing replies. Also, the "Top" button also pops up the forum navigation menu, which I suspect it shouldn't, and similarly, all the page buttons within a thread (First + numbers) also pop up the thread page navigation menu.
3) Using the forum quick navigation from within a thread to go to the forum that thread is in, only takes you of the first page of the thread you're in. For example, clicking the quick navigation link for "Forum Support and Suggestions" while browsing this thread does not take you back to that forum, but to the first post of this thread.
4) The orange feels a bit too harsh, looking almost red when seen next to all the black/dark grey. Maybe go with the softer version of the "Elite" orange used in the game interface background? Plus, that would match my signature image

5) The lines separating the signature panel from the message text in posts are effectively invisible against the background image. Reducing transparency might help, but I suspect the need to be a bit brighter if you want them to be seen. Otherwise, might as well remove them.
6) The reputation button is easy to miss, and also takes you to a different page. Making you leave the page seems a disincentive to giving reputation. The old popup method would be preferable.
7) All posts seem to be padded with a couple extra blank lines at the bottom, artificially making them taller than they need to be - See the space between the last line of this post and the '
Last edited' notice at the bottom.
I'm sure there's more, but that's the stuff I noticed in the first hour. For all that though, great effort! A change of this magnitude will undoubtedly take some tweaking before it's all smooth.