The differences are small, but in the end I don't think it's that important. Get the version you like and for the system that best caters to your needs (controls/sticks).
But if you are REALLY anal about performance and slight slowdown/framedrops. Then it is true. I will say the 360 version is better when it comes to performance. PS3 has a slight advantage on loadtimes.
But for me, the issue of controls/converters is very huge. If I had the same sticks and converters for 360 then I think the 360 one would be the one most widely accepted by the competitive community. As it stands now people don't care enough, but they might if they can figure out what is causing the random lag in certain stages.