Despite all of its flaws, Newgrounds is still the best place to submit animation if your goal is to get it seen and judged (and not just because animations in .swf files look so much better than the formats that other sites use).
Case in point: I recently submitted my first film both to Newgrounds and to DeviantArt. I was just as unknown on NG as on DA, yet it got over 8000 views on NG and 18 on DA.
The one thing slightly marring the experience was that the people who initially vote for movies in judgement seem to be a very different crowd from the typical NG visitor, as evidenced by my film's rating jumping by half a point after it was front-paged (at first it was about 3.64, not high enough to win a daily award).
Still, I don't know of a better site. But if there is one thing I would wish would happen to Newgrounds, it would be for more people from more varying demographics to begin visiting it. A more diverse audience will only help artists, by providing them with feedback from more viewpoints.