There is already an Assassin's creed thread on the forums. It's buried on another page, so I don't blame you for making this thread. I'm going to go ahead and merge it with the other.
EDIT: I have now merged the two Assassin's Creed threads into one. I'm a huge AC fan. Brotherhood is not considered 3. The way the developers have the series planned, any numerical game (IE 1, 2, etc) will star a new Assassin in a new time period. Brotherhood is just the extension of Ezio's story. I think you understand this though, based on what you said. I just felt like pointing it out
Here is an article that discusses possible new features for future AC titles. I like a lot of those ideas. And I think some of them are very likely to happen.
Are you saying that someone else is in an animus many years in the future living out Desmond's life, who is in turn living out the life of both Altair and Ezio? Thats certainly an intriguing theory, but I don't think there's much to back it up. Care to divulge why you believe this? It's definitely an interesting theory, and would turn out to be a very good plot twist. But I'm not entirely convinced that's where the series is heading at this point. Although, it has also been stated that AC is more a franchise than a trilogy. Desmond's story may (or may not) be wrapped up in 3 numerical games, but I have a feeling Ubisoft is going to extend the AC franchise even further. It would make sense for them to do so; it's popular enough right now that if they stopped at AC3, they'd be making a huge mistake, business wise. That being said, I'd honestly rather that Ubisoft not annualize the franchise. It's worked out so far, but somewhere down the line I fear they're going to make a mistake. Or, more likely, the franchise is just going to enter franchise fatigue, at which point Ubisoft should just let it rest for a couple of years.