In general, I haven't had much issue with the new cooldown animation, but there's one thing that amuses/annoys me.

Before, it was difficult to tell with longer cooldowns if they were ready or not, because the last few seconds was such a small portion of the total cooldown timer that the sliver of cooldown remaining wasn't visible anymore. So I'd try to hit, say, Vengeance or Infuriate, and it wouldn't activate.

Now, it's almost the opposite. Since you can "queue" ability use to a certain extent (most visible for mages, where you can hit your next spell before you've quite finished casting the previous one), I've found that I can hit skills and/or cooldowns before the cooldown animation is gone. Currently, it's mostly amusing, but I can see it becoming either something I get used to and forget about the issue or something that annoys me more and more ^^;