I love Revelations in terms of story. The Desmond stuff is interesting but ultimately disappointing. I was wishing for more with Subject 16 and it was implied that Desmond would have an entire city/area to play around in (designed like the virtual reality rooms in AC2/ACB) but the ultimate realization of those segments sucked.
Though in terms of story, it was fantastic for Ezio and Altair's tales. I liked that they tried to tackle themes like getting older and searching for more in life. In Ezio's case, they showed his desire for a life beyond vengeance. Altair's story meanwhile was even more tragic and we witnessed his exile, return, and then his death (that bummed me out, man). On a personal level for the Assassins, it was a great send-off. I loved being able to witness the entire life of Ezio and the huge moments in Altair's and the change. Say what you will about the insanity of the AC series overarching storyline, but I think they do character development really well. It's one of the few games that we get to see a character's entire life, birth to death (in that CG short film included with ACR).