I find this question increasingly hard to answer, as time goes by.
Each Mass Effect game is great in its own right. I enjoy every game of the series. Each improved upon the last and each single one is fatally flawed in one way or another.
If viewed as single games (not connected to the trilogy), ME3 would probably win, even though ME2 has the awesome suicide mission.
(Though, I find the ME series/Shepard trilogy only really works together, as trilogy. It then wins over every other game series I know out there)
In the end I voted ME1, as it spawned the whole franchise, and needs some love too. Besides, ME1 has the most coherent and 'working' universe of all games I ever played. Unlike the other entries, I never had the feeling that what I saw in that game was everything in/to the galaxy.
That sense of a vast, working universe, that does not rely on the player character to live // exists without being actually seen, was somehow lost in the other 2 games, I find.