I do prefer Horde lore to Alliance but if I could join a neutral mercantile faction like the Steamwheedle Cartel I would. This conflict between the two is so lame and forced now, especially with the looming threat of the Legion.
I would rather play a faction that had unique access to both the Horde and Alliance AH's and make gold playing those two markets off of each other instead of actually fighting for one or the other. Just make Gadgetzan the capital, it's got an AH and a bank. They could add fast travel between the Steamwheedle hubs via teleporters, I mean Goblins and Gnomes run this thing. It would be awesome to teleport to the Steamwheelde cities all throughout the content. If they limited the faction to just Gnomes and Goblins, I would have no problem with that.
Personally I think invasion zones should be flagged as Sanctuary for the duration of the invasion and a grace period after. Just flat out disable World PVP. It doesn't make any sense to have some petty faction dispute in the middle of repelling a demonic incursion into your world.