Would an animated series be hour-long episodes (as with live action Trek) or half-hour ones? That would put a dampner on what could be done in a single episode, though story arcs would work just as well.
An animated series might have to be more action-orientated (but seeing as how that was where VOY and ENT were going that isn't anything new), to draw in a wider audience--lets brain-wash some kids to appreciate Trek in all its greatness
As for the comment made about droids and Jar Jar, well a Trek cartoon would remain Trek, just animated. There are no droids and annoying alien characters are confined to the Delta Quadrant. It would be another look at Trek in a very different format, which I personally think might suit it quite well.
I do think that if an animated Trek was an entirely new series they would need to do a TOS/DS9 cross, where in there is a small core of main characters (4 or 5), with a large pool of engaging and interesting supporting characters to be used wherever needed.
So long as they got the setting, characters and stories right. That is what needs to be focused on no matter what format the next series takes