I really liked the ending. Anyone who'd read interviews with Lindelof and Cuse would've realised they wouldn't go into intense technical detail about what the island was - they specifically related to how they felt the devolution of the Force into "midichlorians" in the prequel trilogy of Star Wars was a bad move, and I agree. Having the island still be somewhat mysterious makes a lot more sense than explaining every last detail, because life is mysterious.

I think the finale was almost as well executed as it could have been, given the circumstances. My main disappointment was not seeing Mr. Eko, but I guess that's understandable.

As for my favourite episodes, I'll have to think and come up with a list.