AC3 could've fit well with what I'm talking about, but the game...lacked focus, I suppose would be the best way to put it. If I had my way with AC3, then aside from the core assassin gameplay, I would've started paring away much of the secondary stuff, and really focused in on the hunter/survivalist side of things.
So, the homestead and economy things get cut back, with hunting becoming Connor's primary source of income. Some stuff that was in as a holdover from previous games also gets the axe (the brawlers club being the first thing that comes mind; am I the only one who didn't really read Connor as a 'fight club' kinda guy?). I'd probably also dump the whole tunnel system thing, and handle fast travel some other way. And as much as I liked it, I'd cut the privateer missions, because let's be honest, it really made zero narrative sense in the game.
In their place, the hunters and frontiersmen clubs get expanded, hunting becomes your primary source of income throughout the game, and I think I'd try to come up with some decent survivalist game mechanics for the frontier, needing to keep yourself fed and well equipped to travel the game world.