I came into World of Warcraft during The Burning Crusade, but it was late in the expansion. My first character to quest through Outland was Siori, and when the time came I selected Scryer because (I believe) they had a rep-based Enchanting recipe she needed. That’s it. That was the whole basis for my decision.
In the time since, I’ve kind of alternated between the two factions, more or less on a whim or a fancy. Truth be told, no one even needs to talk to these people anymore and I often don’t. So I really don’t hold any allegiance to either. I’ve never looked up the story between the two sides and as a lore fan, I probably should at some point and perhaps then I will care more. Until then, I just don’t. It’s like the Oracles and Frenzyheart in Sholozar Basin. It’s a conflict that just never did a good job of pulling me in or swaying me one way or the other.