I think the ending worked. The story has the possibility of falling into incoherence, but the ending playing as Desmond was my favorite part in the series, and I would love to see more of it in AC3. Seems like Desmond got all the training he needs, now its time to kick some Templar ass.
I hope we do get to see those lost sequences in one form or another. I think it would be really awesome rolling with the whole assassin team, and with the little amount of time given to Machiavelli, maybe the DLC will focus on working with him.