I think redside has the best story writing hands down. And the unlockable contacts on redside are a breath of fresh air for anyone who is tired of the Issue 1 blueside grinds. It's really odd, but I like the feel of blue side the most, the story of the redside the most, and the artwork, buildings, and set pieces of goldside the most.
I think the Tour Guide missions and the Alignment missions should also get their just praise.
Edit: And let's not forget the amazing community content created in the AE! The limits of imagination are hardly constrained in this system and I forsee a lot more content being added in this realm in the future.