I disagree with the O.P. If you make the alien captain a complex, interesting character, you can still have empathy for him, just as you could have empathy for the Cardassians as depicted in DSN.
My own idea for an alien captain was inspired by the VOY ep Tuvix -- a blended being, created in a transporter accident, composed of several of the more familiar aliens in ST, fusing a Vulcan, a Klingon, an Andorian, and a human. You would still have a human element, obviously, and see how this being brings his vastly different experiences to bear on his command style. I envision this character with blue skin and white hair, with Vulcan ears and eyebrows, Klingon ridges and hair style, with a strange outlook on life.
My own idea for an alien captain was inspired by the VOY ep Tuvix -- a blended being, created in a transporter accident, composed of several of the more familiar aliens in ST, fusing a Vulcan, a Klingon, an Andorian, and a human. You would still have a human element, obviously, and see how this being brings his vastly different experiences to bear on his command style. I envision this character with blue skin and white hair, with Vulcan ears and eyebrows, Klingon ridges and hair style, with a strange outlook on life.