So who do you ally with? WoWWiki provides a pretty nice guide of the reputation rewards, which we'll summarize here. Weapon-wise, Aldor reputation will get you a hit/crit/damage/healing staff and a hit/attack power sword, while the Scryers will give you a healing/mana regen staff and an agi/stam dagger. The Aldor provide caster robes, a melee DPS ring, a tank chest, and a mana regen neck for armor -- but the Scryers give you rogue/feral druid leggings, a spell damage/hit ring, tank gloves, and a spell damage/crit ring.
Both sides offer shoulder enchantments with similar stats in different proportions. The Aldor weight their enchantments more toward attack power, dodge, healing and spell damage, while the Scryers go more for crit, spell crit, mana regen and defense. The Aldors give leatherworkers and blacksmith recipes for fire resistance gear (yes, AGAIN!) and the Scryers give them arcane resistance recipes. Tailors get healing spellthread from the Aldors and spell damage spellthread from the Scryers, and the alchemists among us can get a single recipe from the Scryers only.
Unless you have a burning desire for a specific exalted shoulder enchantment or REALLY want to make fire resistance gear, you may want to make your pick based on the equipment rewards. As a combat dagger rogue who happens to be an alchemist, my choice is easily the Scryers for the dagger, the legs and the alchemy recipe. Everyone else may have a more difficult time deciding. And yes, before you ask, you can apparently switch sides, and you can still use the recipes you learned from your first side (though not the equipment.)
What faction do you think you will side with? Or will you just skip the whole headache and head for Karazhan?