An RPG would be interesting... though it'd be a bit hard to integrate an independent character, given that the developers need to preserve the bloodline from Altair to Ezio to *insert AC3 character here* to Desmond. Might be a bit awkward if they need a male and the player chooses to create a female version. They might have to restrict the gender, but appearance and skills could definitely be made customizable.
It'd be fun to be able to specialize in, for example, short-blade, long blade, hidden blade, or unarmed combat. The more points you put into a particular style of combat, the wider variety of techniques that would be available to you. Movement styles could also be made customizable. Acrobatics, stealth, speed, etc.