It's not so much "choosing" a theatre, unless you have a REALLY hot property or an ultra-specific show (Harry Potter, Moulin Rouge, Matilda). After determining the size of the show, it all comes down to availability and the producer's relationship with each theatre owner.
Sometimes the show/theatre match is perfect: the Mark Rylance Shakespeare plays in the Belasco come to mind. Everyone's going to want one of the prime 44th/45th St houses, but the reality is, anything that could fit in the Booth could also play ~12 others. I would think the Cort and Lyceum are the least desirable playhouses, because of their locations, aesthetics, and second balconies (you can't charge as much for the second balc). But Denzel Washington, Scarlett Johansson, and Larry David have made plenty of $$ at the Cort!
(And I can't NOT mention the perfect jewels that are Circle in the Square and the Beaumont. I wish Broadway had a few more houses that weren't traditional proscenium spaces, it would make things so much more interesting.)