Yeah the 360 gamers always say the controller is best (though how many people have tried hooking up a mouse and keyboard to a 360 to play it?). Ubisoft did actually say with this one that their top priority is controller, even on the PC version. Controller was said to be best with all the previous games in the series though and I always got by no problem at all with keyboard and mouse.
When I played Brotherhood actually, I remembered the controls straight off from AC2 and was using them almost instinctively, despite the fact that a long time had passed since playing the AC2. With any kind of controls for these games there will be a little bit of a learning curve initially, but then it becomes second nature. Can't wait to play it personally but my graphics card just died so I'm sticking with an old 4870 (probably won't be up to running AC3 on high) until the GTX700 series launches :-(