Ultimatly, they both give you nice clicky armor. Basically, pick what you think you would like to do....then find a guild that is on that same faction.
The last link leads to the armor.....the ornate armor is the good stuff.
Also, search "Timeline" on the wiki. Brings up a nice list of quests by class and lvl. Not 100% sure but I think it was done by Woldaff. Regardless, a nice tool.
Or if you're not very opinionated one way or the other, find a guild that you like, and kill what they kill. You probably won't be making extensive use of what you can get from either faction until you're in a raiding guild anyway.