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.
A half-hour cartoon would really just cause a story to get straight to the point and eliminate the need for a "B-plot" that runs parallel to the main plot (such things can be reinstated with a multi-episode arc, though).
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
And there's nothing wrong with that in a action-adventure cartoon, really. Hook 'em in as young as you can. A new Trek cartoon can exist in its own continuity for kids like the various Transformers, G.I. Joe
, and comic book-based cartoon shows.