Oh, it's hardly any massive discomfort - it wouldn't put me off from playing on the 360 if there were no other options. But it is noticeable.
If the XBox360 playing experience and the PS3 weren't otherwise totally interchangeable, it wouldn't matter. But they are - so that tiny, tiny inconvenience is enough to make me favor the PS3 version.
And since pretty much everything I've wanted to play on a console was on both consoles, and identical between the two, my preference for the ergonomics on the PS3 was enough to win it out.