It's so hard to say just one as a favourite
In terms of gameplay- Revelations. It had everything the other games had and everything was so much more 'refined'. Things like bombs, Assassin recruits were really good additions to the game and helped immensely.
In ters of Story- AC 1. I prefer AC1 because it was new, interesting and I loved the Ambiguity from the Templars actions. They really made you question whether they were evil or they believed they were doing it for a good reason.
Overall- AC2. While it doesn't beat either on its individual merits the combined effort is simply amazing.