Well Altair is a definately my favourite in the end because although awesome Ezio needs Altair, and if I'm going all philosophicalised, a dependant being cannot be greater than that that it depends on.
lets make a list
Altair:
~Original badass
~Made Ezio's weapons possible (codex)
~Has a bloody shrine!!
~Better name (when spoken, Ezio reads like a robot name so wins on the visual side)
Ezio:
~Badass 2.0
~Cool Weps
~Has a whole town/city state with it's own brothel
~see Altair point 4
hmmmmm =\ Ezio does have a pretty cool version of Altair's armour, I don't know where to put this
mind you Ezio can swim, and even his attacks with stuff like 'Sword of Altair' are badass.... go Ezio you Italian Robot Pimp