Hey, for those who have finished BioShock: Infinite, I do want to make a note.
Though the difference in voice actors between Booker and Comstock may be just so the player doesn't suspect the surprise ending, I have an interesting theory.
Booker apparently smokes and drinks, judging by all the cigarette buds on his desk, the alcohol, and his ability to consume them in Columbia. This would have a visible affect on his person and, not to mention, voice (as he has been doing so for at least the past 22 years, probably heightening in the last 19). Comstock, however and to our knowledge, does not smoke or drink (though we have no evidence either way). He sounds more robust (even in his frailer state), and does not seem to have a true smoker's voice.
This could explain the difference. Booker abuses smoking and alcohol, which is why he sounds harsher and looks rougher. Comstock looks more fair and sounds more healthy due to his lack of abuse. As for Burial at Sea, we see Comstock has taken up smoking and drinking (again, judging by the desk, along with the shop clerk), which is why his voice has degenrated to a quality similar to Booker's (they are the same person, after all).