So this probably seems like a silly thing to be thinking of right now but it is something to be considered.
In most CCG/LCGs you can divide up your cards as you see fit, usually with some organization to them based on Sides/Factions and card type. With pod sets you're not going to want to do that. If they're not in your deck you're probably going to want to keep the pods together and simply organize them by Factions.
I was thinking of taking a page from the way I store Dominion. For each set of 10/12 cards I group them together and stick them in one standard american size sleeve (FFG Gray sized). I tend to use colored sleeves to delineate the sets and that should work nicely for the Faction pods here. I just tried this with 6 Warhammer: Invasion cards and they fit in OK. The problem I had is that while the euro size cards are narrower and taller than these, that group tends to stick out a bit and makes it easy to remove. Because these are the "perfect" sized sleeve they don't stick out at all, and as they are a bit snug it makes removing them difficult.
Anyone else have thoughts on alternate storage methods? Or maybe FFG will just solve this for us with tabbed divideors… I'm not holding my breath for that one.