I think that my only complaints so far are with the private messaging system. I'd love an option along the lines of, "Don't request read-receipts for every single message sent" on a user by user level. At the very least I'd like to see the read receipt pop-up's button messages changed. I'd also like to convince vBullitin that I don't want to save copies of sent messages by default.
I realize there's little anyone other than the bulletin board's software designers can do about those things though. We can (and I plan to) leave comments about desired design issues in the vBulletin Forum. Many have already complained that The pop-up for Request Read Reciept has got to go. I don't suppose you'd consider turning PM tracking off altogether Djinn or Tourguide?
While I fully realize that such things may simply be subject to stylistic code preferences, is there a particular reason for sticking with vBulletin other than the fact that a license was already purchased? Some of the opensource alternatives are fabulous. I love phpBB for example. Yet Another Bulletin Board it decent as well, in my opinion. I've even used the Invision Board extensively at DykeWrite, though I don't particularly care for it.
I can say that each alternative I mentioned is pie to install, especially phpBB. I've set it up on several sites with admins ready to go in under fifteen minutes (broadband/ T3 ftp time included).
In the end, it doesn't really matter. I'm merely curious. The previous version of vBulletin used here (v2.?) seemed quite stable, as does v3.0 so far. I'm not sure that one BB has more features than another but those features are arranged differently and presented in different ways.