From many weeks I've been angry about the server issues and I did a little research of my own and majority of the servers are either Horde/Alliance or dead. I know you Blizzard, are working hard to improve the technology to sort this out but it's getting to the point when the last what was called a 'balanced server' Outland is getting undertaken by the Alliance. There are a few options that are possible with the current technology:
1. You may offer Free Faction changes by monitoring the server population (Horde/Alliance) and then deciding which server deserves it, of course few percent is not a big deal but balancing it to the state where both Horde/Alliance are playable would keep the community happy.
2. Cross Server is a new technology that is currently under the development and as we know it works almost everywhere except the major cities however the problem is it doesn't solve the balance, yes we can see more players in the open world which is awesome but what about the auction house, raiding, guilds, arranged fights, undefended major cities, leveling zones in Pandaria and many more other issues that come with it. Besides what really forms a good faction are the friendly guilds available for players and sadly there aren't many of them on servers 10% Horde, 90% Alliance.
3.On the faction that is way too high in population you might want to offer a discount for those who faction change in a set period of time. This would surely encourage some players to move.
4. You can encourage guild faction changes, so let's say you the Guild Master on the higher populated side and faction change the guild, it would automatically give all the members a discount to faction change, let's say 50-60%. I know some of these options would require you to put a lot of money in this but it would pay back with a happy community.
Others Concerns & Suggestions
1. Human PvP trinket is one of my concerns due to the fact many hard core PvP players will roll the faction due to that trinket. Besides picking race for racial itself is silly and you may want to think about replacing the racials with some unique cosmetic abilities or something along those lines.
2. The guards on PvP servers in Pandaria are actually quiet strong but I wouldn't consider changing that unless you solve the faction balance issues.
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