Though the ending was poorly delivered, I did like 3 the best in terms of story and plot. I preferred the RPG mechanics and sense of mystery in 1 to what followed, but the characters were not as well fleshed out and sort of cookie cutter archtypes compared to their reworking in ME2. I like 3 the best as it had the most sense of scope to me, with the vast war and all of the side plots being tied off, but they really took the feeling of mystery out of the Reapers and Protheans by that point, which is what the first game did best. So....
As a story or for replay:
ME3 > ME1 > ME2
As a video game experience:
ME3 = ME2 > ME1
Also, as someone who does not do much multiplayer gaming, I was surprised at how much I enjoyed ME3 MP. I think there is a great void in the market for a good coop game of this nature.