First of all the Romulus Lair in Saint Peter's Cathedral has a badass ending. Where the cardinal marvels at Ezio saving him from falling only to have Ezio grab the key around his neck and let go
Also I like that Ezio wasn't afraid to use the Apple. (Although it was a bit annoying that it was ALL you could use.) So often the hero will obtain the super-magical plot device but will refuse to use it because "its too dangerous" or whatever. Ezio had the far more realistic outlook - it is too dangerous to leave in common hands, but while I have it and the shit's hitting the fan I'm damn sure gonna take advantage! And holy crap do you kill a lot of people by the end of this game. Seriously, try to think how much death you've actually dealt in the last two missions alone.
Also, bah cliffhangers.
Also also, Altair's armor looked a lot cooler than Brutus'