You're probably right about the mocap because look at VF and Tekken, but even in Tekken I don't like some of the slight sliding that takes place while jockeying for position. VF has incredible movement though.
I'll speak for myself, when I refer to clunkiness I'm specifically referring to the animation, which if you look at certain attacks, like Ermac's flailing arms, they really bother me, because they look sloppy. I'm also referring to some of the idle stances or the way that characters like MK9 Cage have entire strings where he's only punching with one arm, like a SF stand jab, but it doesn't look like a normal fighting jab, because the technique seems wrong. That annoys me a lot because it doesn't look good imo.
The clunkiness I see is kind of like how the fighting can be sometimes in WWE vs boxing or MMA. You know how looping and slow the punches are in WWE so the audience can see the attacks, and so they don't hurt each other. That's how the attacks feel in modern MK sometimes. They feel too choreographed--then there's the flow, or lackthereof of the canned strings. Remember some of the complaints of feelings of having to "fight the engine" in order to pull things off. There feels like a slight hitch between attacks that aren't predetermined strings. I don't like the feel of Marvel 3 either, though(random thought lol)
I just realized, after I had my picture examples and my ssf4 video, that NRS has the sales. Lol. Money talks, so regardless of what looks better in the game I can't argue with 4+ million units sold. I expect mkx to sell just as many or more.