Overall, there are far more alliance players, than horde players. So overall, alliance gets longer queues.
Back when it used to be server only, there were exceptions. The server I started on (EU Bloodscalp) had a nice 1:1 ratio, so queues were very short for both sides. Then the server overpopulated, and free migrations opened, first to EU Twisting Nether, and when the server stayed overpopulated, another was created to EU Trollbane.
A lot of Horde decided to pick up their roots and move to Twisting Nether (from various servers), while the Alliance was less inclined to move. The result was like a 1:4 ratio (A:H), so it was one of the few servers where alliance had instance queues and horde was doing the waiting.
Later on, when Trollbane opened up, the alliance finally decided to move, resulting in a ratio on Trollbane highly favoring the alliance. On Trollbane, the exact opposite of Twisting Nether occured.
The crossed battlegrounds evened everything out. They made it so that the total alliance:horde ratio for all groups was about the same. The result is more alliance than horde on every battlegroup groups, so all alliance now got queues (though for some, not as drastically as before), and all horde get to join near instantly.
For some reason, the ratio in our group adjusted after applying the group system, as queue times became shorter and shorter.