I actually bought a japanese Wii and pre-ordered this game when I heard about it. This was partly because at the time it was looking like it was NOT coming out here at all and I had to have it. Of course it obviously did come out here much later...and I then bought that too
I don't regret it though because there are a few differences in the american release...a few different characters being the biggest, but they also changed the opening, took out the animated endings (this made me sad cause so many of them were awesome) and have completely different music. The music is up and down...I like some of the tracks for the US ver, but the coolest thing about the japanese ver was that it had character themes for music (just like MVSC 1) that changed up whenever characters came in. Oh, and the jap ver also had different mini-games for each character.
Personally I use the classic controller...I've been playing fighting games since the Sega and SNES so I'm much more fast and efficient with the controller as opposed to a stick, though I can use them ok (have a nice Hori stick). As far as characters I use Batsu almost always, and the 2nd character depends on my mood...Roll, Megaman, Zero are often picked, but almost always Karas is my number 2 guy.