1. The chances of Kirk being resurrected from the dead are more likely than this scenario. Cost and viewer connection just wouldn't be enough to justify it...but I think you know that, hence throwing out this extreme example of an alien.What if the alien was a Tholian, remember the Tholians from the series Enterprise? Now we got an idea of what they look like and what sort of environment they live under. So how would a Tholian be as Captain?Huh? There's plenty that can be done. Just take a look back at the movie and show Alien Nation. One main character is human, the other main is alien. You actually get the perspectives of both AND learn about how similar or different "George Fransisco's" family and species are in contrast to humans. Another example - Delenn from Babylon 5 is (arguably) a main character in Season 1, and during this time, we get her alien perspective on events which take place.Well what can you do besides have forehead ridges or pointed ears? Spock commanded the Enterprise on a number of occasions.
The concept of an alien captain can certainly go wrong, but only if the writers follow your assumption that they are just humans in weird make up...
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2. Tholians are xenophobic + a hive-like species. They probably wouldn't do it on principal alone, never mind species psychology.
3. Even if it were something that a writer and studio decided to do, this would be a perfect scenario to have the 1st officer as the main character, thus his interaction with his alien commander could demonstrate command style differences, similarities, conflicts and resolutions regarding misunderstandings of cultural/species differences.
Hmm, and here I was thinking you had this "can't do it" attitude. I actually have a "dwarf" size character as one of my STO captains. He belongs to a race which is respected by both Feds and Klingons for their tenacity...but that's all I will say about my invention...Here's another interesting choice, how about a Hobbit? I mean seriously, somewhere in the Trek Universe there's bound to be a humanoid that stands 3 feet 6 inches tall as an average sized adult of their species, so how would such a diminutive race fit into the captain's chair?