Hmmm....
This is a tough one.
I'm going to have to go with Mass Effect, but only just, and the reason why is something I can't really explain. It just felt more...er...more.
The Citadel really felt like an enormous space station, the guns felt more real (the tinny, rattly sound of gunfire in ME2 is not nice) and the Mako added a sense of scale that ME2 lacked.
I didn't find the combat to be that much better in ME2, the power system sucked and the ammo system was incredibly stupid. On the other hand, I much preferred ME2's modular armour system, and only wish they could have applied that to the weapons. The characters in ME2 were much better, but the story was significantly worse, and just raises questions, such as why was Sovereign working with the geth when he already had a race of hyper-advanced fanatical devotees at his command? They also kinda screwed the continuity over. For instance, Joker. In Mass Effect, he only had brittle bones in his legs, and said he could only get around with the use of crutches and leg-braces. In ME2, you nearly break his arm when you lay a hand on it, but then later, Joker's walking around without crutches and even being thrown onto the floor without being severely injured.
I love ME2, but it feels sort of washed-out and thin when compared to ME.