Spoiler alert, the last sentence :P Also I'm sure the ending was deliberate.. you know they're going to milk this franchise until it's dead. Not that I'm complaining, I'll keep buying them until they start to stink, which hopefully will be a long time coming.
I've always been a fan of the Assassin's Creed games, however ACIII felt like a completely different games. Not in terms of gameplay, but the atmosphere it had. The feelings I got from the previous installments didn't reoccur with ACIII, where Altair and Ezio made me feel like I was at the center of something big that I was the conductor for, where sides were drawn and it was me or them. Connor made me feel like I was witnessing a series of events beyond my control and was in some cases helpless to do anything about. Sort of like no one was listening despite trying to do my best, which fits in perfectly for the time the game is set in. Instead of their being a definite good and bad side it was more like Connor is caught in a constant guessing game of who is the bad guy to the point you start to question everything you have learned in the past few games. Especially concerning Templars. For one I no longer think of the Templars in the same way as I did, especially considering that there are bigger things to be worrying about. Those of you who completed the game should know what I'm talking about.
The only thing that annoyed me was the anti-climatic ending given to Connor's story. It also seemed like some things were suddenly thrown in there too, especially in the lacklustre way Desmond's story was in general presented. Possible due to them having to spread Desmond's story over an extra two games (Brotherhood and Revelations) instead of the orginal intention of having all those events take place in ACIII.
But on another note it appears that while this is the last AC for Desmond it doesn't appear to be the last in the series.