So, this is how 2012 looks like so far, manufacturer-wise:
Yamaha is the best bike; the 1000cc engine has provided the power it lacked, and they have excellent riders (four of them, all on factory spec bikes, like Honda last year). Will they beat Stoner? No way unless Stoner helps them, but they can beat all others.
Honda has some problems with the new tires, but they also have Stoner, who can work around them. Unlike last year, now it seems the best bike only when Stoner rides it. But it can compete with the Yamaha on all tracks, and HRC has huge resources on tap.
Ducati: they have changed the frame and it is better but it still needs to be ridden like a Ducati, and none of the current riders can do that completely. If I were them, I would focus more on Nicky and Barbera, who at least seem willing to give it a try. (Wait; maybe, quietly, they are doing that already...?)