Arch's link sums it up pretty well(though I don't actually have a problem with Pain's face being superdeformed by the Kyuubi's punch, that actually makes sense).
My primary complaint with the animation in the beginning is they make the Kyuubi look like 3rd Gear Luffy, which works in One Piece because One Piece is crazy fucking ridiculous. Kyuubi's not supposed to be comical.
Like I said earlier, it get's much better right about the time Kyuubi breaks the necklace, and the episode is pretty awesome from there on.
Even one second can completely pull you out of the moment if it's jarring enough.