The 360/PS3/PC version or the PS2/Gamecube/Wii version?

I would have to say the original Xbox. The story is better and has good graphics (Xbox 360 has better but...that's my opinion).

Only...Some missions you have to KO/Kill some people..like in the Money Train mission.

P.S. Walking on top of the train was pretty fun.

I played through both of them at all the difficulties and I have to say I enjoyed the Xbox360 version more because there are more moves, gadjets and the graphics are better as well. I do however like the PS2 versions coop. I think the other version should have that as well.
I own both versions though so I'm happy.