I can only assume that people who votes for Azureus haven't used Transmission...
I've used both, but I currently use Azureus. I used Transmission for quite a while before switching to Azureus. I don't know the cause, but Transmission is just slower than Azureus. It might be that the code is buggy or perhaps Transmission is still banned by some trackers. Whatever the reason for the slowness, I chose function over form and went with Azureus.
The main annoyance I have with Azureus is that instead of having a Dock menu, it has a menu bar item that functions poorly. And if you do without the menu bar item, when closing the window the application stops transferring (essentially quitting).