In a dilemma of which one I like best... hmm...
Discovery
Side-tracked, but great on its own
Resolution
All good, for different things. The novelty never wore off of ME1 for me the first time I played it... even with the recycled buildings on all the side missions. I loved it.
ME2 was like a parallel universe adventure, but still loosely connected to the story. Only in hindsight though. Didn't know that first time I played it. Loved it for the gameplay changes too. Combat was more fun for me. But I did miss the Mako, and I never thought that would happen.
ME3 was just ... wow, I dunno how to explain how i feel about it. Bittersweet, I guess. But I like the gameplay improvements, and the number of variables that go into the story. For those two factors, I think it's the best of the three.