Halo 2's story is much better in my opinion than 3. I think 3's story, while still good, was probably the weakest of the trilogy. I don't like that Cortana didn't accompany you throughout the majority of it, it didn't feel right. And basically wiping out the parasite was your main objective all along. The Covenant was just there, almost like a we're in your way now for what you need to achieve approach.
As for multiplayer I don't care for either. Halo Reach has the best multiplayer for me.