I'm not sure who I'd want as the new Captain, but I would really love to see Ron Pearlman (Beauty & the Beast/Hellboy) as the Chief Engineer.
Maybe Joe Flanigan from SG-A would be an interesting choice as the Captain.
I know, I too have been thinking not just in terms of a captain but a full cast list.
Amy Ryan as the captain. She can play a deadly serious professional, who commands leadership and respect. But she can also be surprising goofy and charming like as Holly, Steve Carrell's love interest on The Office. That sort of versatility would keep a female captain from becomeing dull.
Titus Welliver who played Silas on Deadwood as well as the "Man In Black" in the season finale of Lost last year. Not as the capatin but as Ryan's first officer. I like that dynamic of a feminine, intuitive Captain supported by her grizzled badass XO. It would be similar to the (intended) dynamic between Janeway and Chakotay on VOY. But in practice like Adama and Tigh's relationship on BSG.