I have been thinking this for a while.
Star Wars has proven that, done right, an expanded universe in animated form can be fantastic cannon for the mainstream films etc.
There is also many benefits to this, especially setting it in the OS era, as you could get a couple of the key cast back to reprise roles (like Shatner)
However, the main problem is Paramount. They are very precious when it comes to their Star Trek franchise and maybe dont want it to appear on something like Adult Swim or Disney. Although on a mainstream channel I think a Star Trek animated series would be brilliant! and like they have done with Star Wars, they could link it to all their live action universes easily!