Actually, I remember seeing some jive talk on kotaku that they got scuttlebutt from Ubi that they were thinking of yet another time period to Animize Desmond into.
Frankly, I think this is the best road to go. Yes, Desmond now knows how to shank someone, but to be honest, that'll only really pass muster if you live in the 15th century or earlier. Despite the rather stick-loving brigade of dummies you put up with at the end of AC2, I'm sure the modern Templars are well-versed in the use of firearms, and no amount of fancy shiv-work will help you against a brace of automatic rifles, hopefully firing lasers of some sort, given how this is the future.
So, my prediction is that Desmond's next foray into his priors will involve either something more modern (perhaps his own father or grandfather), or perhaps even a series of time periods as you go running about looking for more of the Pieces of MacGuff-o-matics.