Appreciate the write up. I feel the same way about a lot of your points, especially regarding the story and cohesiveness of the whole package. PoE is a neat idea but I still expected a lot more as far as presentation and challenge goes. Despite being different every week, it's gotten somewhat stale to me. I think it's just the general claustrophobia of being confined to a dark room with adds on all sides and not much happening as far as map traversal unless you're fighting Skolas.
On that note, Skolas void burn is one of the better encounters in the game. It's held back only by the holes with the entire PoE design and of course Destiny's enemy behavior in general. But it's the main activity in PoE that I've enjoyed.
If nothing else, hopefully Bungie has figured out a new way to design encounters for the next Raids.