They should be neutral, IMO. If you play as a Venthyr for example who decides to venture into the mortal realm and acquire anima for his/her self, you should pick a faction that you think best meets that goal.
I see a lot of arguments about which side Kyrians etc should take. But it makes more sense to be neutral like Pandaren.
IMO:
-Nightborne should have been neutral (received aid from both factions)
-Highmountain should have been neutral (received aid from both factions)
-Dark Iron should have been neutral (got treated like shit by Alliance for ages)
-Mechagnomes should have been neutral (received aid from both factions)
Heritage gear could have two different colours depending on faction.
Thoughts?