From what I've heard from the YaBB 2 guys, most of the code and presentation has been seperated to the extent possible and the code has been cleaned up, supposedly. It's much more efficient with file I/O than it used to be.
YaBB doesn't support threading, because most widely used BBS systems don't. Look at vBulliten, SMF, phpBB, etc and none of them are ever used in threaded mode, even if they do have support for it. If there was massive user demand for it, we would consider putting it in, it's just not something that our users want, so we focus on other things.
I believe you can be a member of multiple groups with core code now.
The next version should be better, but it's going to take a lot of work to finish. Even then it won't have threading, unless, of course, some people here want to add support for it, once I get the base code stabilized/fixed. ;-)