They would still be separate

They would still be separate. Not much would change for the one with short queues. Alliance would still mostly face horde. I feel this would really even out the winrates as horde who win 80% of their games may be knocked down a peg since they would or world of Warcraft also face other horde groups. Alliance in av/ioc would be knocked down a peg as well, as they would likely face other alliance teams in most matches. I see no harm in it.