No, bad animation is not made more acceptable because everything is animated. If it looks like bad animation, guess what, it is. That's how it works. EVERYTHING in movies and tv is basically animation since it's all just a bunch of images being displayed rapidly frame by frame. So the area of difference is become more minor now with cgi getting better.
Animators wouldn't have to check every frame for consistency if it were believed we couldn't decipher so easily if something was badly animated. And whatever rules are established for the animation must be obeyed. Final Fantasy Advent children containes some very good animation for instance, but just as in live action I can easily tell where the movements were more unrealistic compared to their normal animation. Go watch the movie yourself and come back here and tell me because it's all cgi, everything looked natural and smooth. At times, yes. At times, no. Was that the animator's choice, to bend the rules for that extra something however? Absolutely. Does that make it more acceptable and less fantastic? No, they wanted it to look fantastic so they took the liberty they have to do that... it's a videogame movie. And we can tell, easily, when they take those liberties...
Stick jar jar binks in final fantasy and there's no way in hell he'd be acceptable as part of that world, even there.
And that's what I'm saying. Bad animation is still bad animation.