The main difference is that Armada mostly makes higher end skis while Line makes price point skis too. Of course comparing something like the AR7 vs. the Afterbang won't make any sense because the Afterbangs cost significantly less. In my opinion if you're comparing something like the AR7 vs. the Chronic, it's impossible to say which one is better quality-wise.
My opinion is that if you forget about the cheapest Line skis (and they're not THAT bad either, but you get what you pay for), both of these companies make very good skis. I only have Line skis but I would have no problem buying Armada skis instead.