Since they are both Adobe, I suspect they are pretty much the same (at least for CS5.5 and CS 6.) If you have a shot that is difficult to stabilize, I'd suggest googling for some advanced tutorials. I have had shots that seemed impossible, but Warp Stabilizer handled quite well, just needed a bit of 'fine-tuning.'
Another option would be to convert your mts file into something that Mocha can handle (avi or image sequence if I recall.)