The reason it can track the trails of people is because Ezio can now see the footprints of enemies, as well as where those enemies are intending to go. It's really just an extension of the original system: he used to be able to see what their intentions towards him were, now he can see what their intentions to physically do are. Also, with Eagle sense he sees enemies by sensing vibrations, not visual sight, so he can see enemies through clouds of smoke, in dark environments, and through certain obstacles. It uprgrades his hearing too, so that he can eavesdrop on guards from far away, and hear their heartbeat to find out how nervous they are.
But yeah, Eagle sense is a "real" ability, it's not connected to the Animus.
I would say that this is the most significant sequel AC has ever gotten, in terms of base mechanics. And lets not forget, it's not just about the mechanics, its about how you use them in the game, or the structure of the game. With the various missions types being honed into several really enjoyable categories, that's probably going to be the best part of ACR. There are several types of missions: Templar agents (side assassination missions against each of the multiplayer characters, including full backstories and investigations) Story missions (which will run the gamut from Uncharted style setpieces to sneaky stealth action), something akin to the war machine missions from brotherhood, and something like the Assassin's Tombs and Lairs of Romulous, as well as Virtual challenges and Desmond puzzles.
However, backing that heftly lineup are things you can do at any time in the open world: random events (as you walk through constantinople, you will see people doing things that might be considered unsavoury, such as guards oppressing civilians, theives stealing from shopkeepers. you may choose to step in, and for that you will get a reward, which could be bomb ingredients, money, or something else.) and Assassin's Dens. (an upgraded version of the Borgia Towers, these dens will now have greater variety in appearance and Templar defenses, and once taken over, Templars may at any time actively try to take it back. You will be notified, and can either hope that your recruits can handle it, direct them in battle in gameplay which is supposed to be like an RTS, or get in there and personally show them the way out.)
So you see, this game may be the AC game which changes the most about AC. And the story of all three characters involved is more intriguing than any other AC one before: The grizzled veteran searching for a purpose, the legendary Assassin, leaving a message in the form of his most important memories, the victim of fate, trying to escape the prisons of his mind through accepting the will of a machine.
And yes, I know too much about this game. I just really like AC. : )

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