Yep, changing the factions doesn't really fix anything, it just makes the problem worse and probably permanent.
Nah eventually it will even out like it did in WoW. Alliance was so bad that everyone faction transferred over to Horde as soon as they were made available except for a few of us who stayed just for the challenge. By bad Im talking 20-25 losses in a row bad. Eventually because so many people faction transferred, mostly our bads we started winning more. Also again because so many people switched to the other faction their queue times went through the roof. Ours were near instant while Horde had to wait a lot longer for queue to pop. So then all the good PvPers Horde side faction transferred over to Alliance to escape all the bads that were causing them to lose more and also the long queue times. Now Alliance wins a lot more and Horde loses a lot more. So things will eventually even out just have to give it time. By time I mean 2-3 years cause thats about how long it took in WoW for Alliance to get better.