I think a lot of the "problems" with Lost stems from the writer's strike. They ended up losing a bunch of episodes with that. Also, I think the writers were just adding mysterious things in without really having answers to them, hoping they would be able to put in answers later. Once it became clear that Lost was heading in a more religious direction (good vs. evil, purgatory, etc.), they probably figured the sci-fi questions weren't as important. While I wish a lot of the earlier sci-fi stuff was answered, I still think the finale was a great episode. I like to think of Lost as being basically 2 parts, seasons 1-4 and then seasons 5-6. 1-4 was a lot more sci-fi while 5-6 basically focused on Jacob & MIB and the other religious stuff. Looking at it that way, I think both parts were very good, though the first couple seasons were obviously the best.