I agree with OP entirely. A year ago, there were many PvP guilds on Horde, now there's two or three.. They all go Alliance because they can VS each other, and do things that Horde faction simply can't do.
Regardless of how many people are in queues on Horde faction, Mercenary mode will never work the opposite way. It's only Alliance > Horde, and not vice versa. All the OP and his supporters (myself included) are asking, is that it can work both ways (Alliance > Horde, Horde > Alliance), so we can do all the same things the opposing faction is doing. It's only fair, if you really think about it.
As someone mentioned in a previous post... entirely removing Merc Mode might actually be of help also (if the current request can't be implemented).. A lot of people might not like it at first, but it could eventually bring some kind of balance to factions.. Horde PvP is pretty much dead at the moment, with the exception of WTF Unity, Not Sorry, and smaller guilds like Puff Puff Pass.
TL:DR
Merc Mode for both factions, or for none.