I actually just finished AC:Rev today myself. I have to somewhat agree although Ezio realizing who Desmond will be and how his ability to see Altier's memories might some day be seen by a later generation was quite cleaver.
That being said this game had 2 of my favorite AC moments. Ezio dressed as a minstrel and making fun of everything was hilarious and the developer transforming the horse cart battles (which I hated in every incarnation) into something truly exciting and something I wasn't expecting at the end of AC:R. But yes, everything involving Desmond just seems tacked on. Even the extra 5 or so stages just seemed like an odd mess with mechanics that seemed nonsensical and pointless, just to do something else.
also I didn't hate the tower defense stuff, although forcing it into the regular flow of the game was kind of dumb. Having that tower defense as something I could fire up when I wanted to do it would have been better as it was fun/interesting outside of the context they tried to put it in.