I'd want a truly alien captain--cgi, costume, or whatever--voiced by a deep baritone actor. Something hideously strange like the Alien, something wonderfully fantastic-looking, or even a series alien we've seen before. No more humans; they're getting stale.
It would be too hard to relate to a truly alien captain, or a main character for that matter. They are better as villains or as something like the Xindi-Aquatics, depending on what they look like. Besides, Trek is about humans and not aliens. I personally would like a human captain.
Michelle Forbes would make for a great captain, although I doubt she would take the role, as she was supposed to be on both DS9 and VOY.