I honestly don't see the issue with not being able to get literally every neutral upgrade from the expansions of a single faction. Nothing they have put out so far is so powerful the other armies can't compete without it. It isn't like Waiqar and Daqan will suddenly suck because they don't get that card. It adds variety to the game, and that is a good thing.
The caveat to this is that the neutral upgrades stay balanced enough that they don't invalidate a faction if it doesn't have it. If you have to have a neutral upgrade to compete and it is only available in one expansion box that will be a problem.