I dunno - I'm not saying the animation is great technically, but I think it's got a certain style to it that I like.
But it being animated really does open up the stories to be far more science-fictiony than the live action show. Besides having actual alien looking aliens (since they don't have to be guys in suits or with makeup), they can visit very strange planets, have things like flying aliens/monsters, a lot more action scenes, etc. (Yeah, they could do that with CGI, but cheap CGI looks terrible, and out of place compared to other stuff).
Number of seasons aside, it's a shame they only made 22 episodes of this. I really think they should consider making new ones. I noticed that the show seems much more open to giving the lesser characters a starring role as well - Uhura gets a lot more screen time, Sulu too. (Chekov seems to have disappeared, though)