Generally the scenes are rendered via 3rd party software to obtain better lighting and surface effects. Although we have seen in engines like crysis cryengine, there is the possibility of rendering and saving images at specific frame rates and not in real time, much like a professional 3d render. It could be possible the footage is rendered using the game engine using settings designed to max IQ and save the video to be played back later in realtime. The reason I don't think this is such a well developed client function would be easy to find and unlock like it was in crysis, but you never see it.
The AC2 movie obviously used custom assets, but AC3 and above generally used in game assets with possible acceptions for the main characters. For instance the bloke in the AC4 scene that gets pick pocketed, the original model was probably not designed to have the outer clothing pulled away and was not originally setup with such a high tessellation count to do so and look good close up. Pyrotechnics and particles are also usually not the games original.
A fair amount of game asset animation is motion captured (heck these days, selling motion capture data is a business in itself) but these trailer scenes most likely contain unique motion capture to the scene itself and it is not a scene in the actual game.
What makes things difficult is in the end we can look at something and go "yea..I can see that being done in game" and yet in reality the editing process is discovered to be super involved and uses over a dozen layers in a scene that you never realize. I always think back to the making of the WoW Lich King intro. While watching it you can recognize the individual assets and think "no big deal, they rendered up a mountain cliff, some models, threw in some animation and out pops your intro" but in reality there was a hundred or so layering tricks and 2d effects used just to obtain a look in certain shots and to avoid needing to render something that the team deemed would take to much time to do.
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