I've got it! Chi McBride ("Winston" on THE HUMAN TARGET) as the Skipper. He's got the right build and he does slow-burning exasperation well.
It's an intriguing idea, and I'd love to see McBride do a funny grouch like Emerson Cod again, but I'm not entirely sure. There's an anecdote from the casting of the original show -- they wanted to make sure the Skipper would remain likeable no matter how mean he got with Gilligan, so they really had their candidates pour on the abuse in the auditions, and Alan Hale, Jr. was the only one who could pull it off without going too dark, too mean. No matter how mad Hale's Skipper got, he was still a big teddy bear and you were never scared for Gilligan. But McBride can be a pretty intimidating presence. If he could strike the right balance, it would be a great choice, but it would be tricky.