I believe the producers considered making Sisko an admiral, but thought it would take him out of the "pantheon of captains". Frankly, I think they should have anyway. They were original enough to start him out at commander, and I think it would've been cool to have a main character reach flag rank in a series rather than a movie or an alternate timeline or fantasy.
Even if Voyager's computers had the latest info on the Dominion (and they had enough info to use Jem'Hadar ships in holodeck simulations) there's no reason to think the Doctor would bother knowing anything about the Dominion. Clearly the Doctor isn't completely tied to the computer, since he interacts with it by terminal rather than some kind of "mental interface".