In a word: Yes. the current state of animation offers almost endless possibiities.
Look at what they did with The Clone Wars
animated series. IMO, they really did a good job of expanding upon the live-action movie series. The same thing could certainly be done with Trek.
An animated Trek series could be set in any era, with any characters. You could have stories set in any of the series, or veer off into new characters and situations. With the right voice actors, you could even do TOS episodes.
It could even be an "anthology" type series that so many folks seem to advocate (but couldn't really work with a live-action format).