I agree that unrealistic behaviors are necessary. Yet, I think they were less jarring when characters were just blobs of pixels or blocky piles of polygons. Now that they are animated through motion capture, voiced by professional actors, made of a gazillion polygons (and that you could see every pore of their skin if you zoomed enough), unnatural behavior can really stick out.
Another factor might be the camera. Here's Link against Stalfos in Ocarina of times. When Z-Targeting is used, the camera follows the action closely, it's very dynamic, so you're less likely to pay attention to the other Stalfos. Moreover, it seems to me that the other Stalfos actually tries to get out of view.
Whereas in the AC gif posted above, the camera stays farther from the action, so it's more easy to be distracted by the other enemies (but I'll say it again, I have never played an AC game, so I'm only judging the gif).
I just think the AI needs to react to explain it a bit more, that's all. When you are flailing away swinging your sword every which way, it makes sense some of them might stay back and "wait for an opening". When you are busy bleeding someone out and there's an obvious opening, they should animate some kind of recoiling in shock and horror, blanching, maybe throw up or something, that would give a somewhat plausible reason why they don't attack. Just standing there with a clear opening and not doing anything is what looks weird.
And yes, camera stuff can also really help, like changing angle and maybe even applying a strong depth of field blur during the cinematic kill can help hide this. Plenty of other games have used techniques like that (pretty sure the recent Shadows of Mordor uses both AI reactions and camera tricks to hide it when you do a finisher move).
Anyway I probably shouldn't have said anything, totally off-topic, just really got to me when looking at that gif. Sorry to derail.