I'm currently playing Far Cry 3 and Assassin's Creed III. To be perfectly honest, while they're both almost equally fantastic games, I think out of the two I may have to pick Far Cry 3 as the prevailer. This is because Ubisoft spent a solid year hyping up Assassin's Creed III as something stupendous, something utterly extravagant, making it look like the greatest game ever to be released. In the end it wasn't. It was a fantastic game, but not on par with what they were hyping it to be. It let me down a bit. While the game itself is very inconsistent (some missions are really fun, some are incredibly boring), the story is still great all the way through.
Far Cry 3 on the other hand surpassed my expectations by far. The FPS stealth is so incredibly dynamic and expansive so that it never gets old; there's always a different way to take out that sniper with the alarm or that gunman guarding the captive, whether it's tossing a rock at a barrel to deter his attention or swinging in from a zipline and landing on top of your foe with a knife. The possibilities are endless. On top of that, it accomplishes exactly what it's trying to: you feel like a very mortal human being. Three or four bullets will kill you, and the sound effects along with the immerse camera can genuinely intimidate you when you're against a large number of enemies.
The two games actually share a lot of similarities when not focusing on the core gameplay aspects. In both games you can hunt and skin animals, sell their hide, loot bodies and containers, and you have loads of different kinds of assassination techniques, right down to ziplines themselves. However, Far Cry 3 actually gives you more initiative to do this because of the whole crafting thing: hunting certain animals and plants allows you to craft items like weapon holsters, syringes, drugs, and so forth. Far Cry 3 actually makes it something really important compared to Assassin's Creed III. This is ironic because hunting is part of Connor's (ACIII protagonist) culture, and it forces you to skin every animal because "Connor skinned every animal he killed" instead of giving you initiative to do so like you're given in Far Cry 3, where you're just a guy trying to save his friends from an island.