I'd suggest you get the same Faction with em, simply because its easier to quest that way. Bunch of the quests in Shadowmoon and Netherstorm are specific to either Aldor or Scryer, so having to do both sets for half benefit would be a way to waste time, I guess. If that made sense ^^

If your concern is with not being able to use half the rep items you come across, then I don't think you should be troubled. It's fairly easy to trade either kind for the other, and failing that you can always sell em.

Also, with regards to which faction to go for, the deal breaker is the Shoulder Enchant. Scyers is better for Fire mages, Aldor for Frost. Marginal difference, sure, but its there