Well let's look at the pro and cons of an animated series vs. a live action series.
An animated series would have a smaller budget and could create more fantastic alien designs.
The biggest problem with an animated series is the Animation Age Ghetto. http://tvtropes.org/pmwiki/pmwiki.ph...ationAgeGhetto
Now Star Trek is not some super dark series and I do think most of the Star Trek episodes are fit for whole family, not being said I would hope some greedy exec wouldn't try to use a Star Trek cartoon to talk down to kids and try to sell them toys. I will say I think TV animation has improve a lot over the last 20 years, starting with the introduction of BTAS.
I think an animated show would have a faster pace then a then a live action, but if handled well perhaps it blend high paced action with heavier concepts, similar to what BTAS, Gargoyles and Avatar did.