I wouldn't mind a Clone Wars style for Star Trek. The characters are stylized, but still recognizable. Toss in some really great writing backing some solid story concepts. In fact, the Clone Wars production tream would be my dream team for a ST animation
UGH!! I HATE THAT STYLE. Its lacking detail and actual ANIMATION.
My dream team or the guys who did BATMAN THE ANIMATED SERIES from the early 1990s.
Or Perhaps the Team that did GARGOYLES . Both excellent quality animation.
as for anime, I think that would actually be best, if you avoid the big eye stylized crap. Take a look a "Ghost in The Shell" or "Cowboy Bebop" ...especially Cowboy Bebop. I think Star Trek would work great in that format.
But for the love of God, NO MORE FREAKIN CGI SHOWS!!!