I think there was a lot of great stuff in this one, what's already been mentioned, like the excellent visuals, the little bits of humour, etc. Personally, I LOVE Charlie so any visit to the alt-verse is welcome as a chance to see him again. I think it's given us more food for thought about Walternate and his agenda, that's for sure.
The problem with the last two episodes and why there's so much negative reaction to them, is, IMO, because human beings tend to remember best the end of things, the last thing they saw/experienced. So, even if we liked Charlie and bug girl and felt bad for this or that character or ooh'd at the zeppelins, if we didn't like the ending, that's the thing that sticks with us. We have to work hard to remember the stuff we liked that came before it.