I threw this out in the announcement thread. If we're going to keep both damage decks legal for tournament play, then a better way to implement it would be to have you switch decks with your opponent before each match.
Instead of simply choosing the deck that does the least amount of harm to your build, you're instead able to select decks based on what you expect to see. Expecting a lot of TLTs and Palp + 2 Aces? Bring the old deck, where Munitions Failures and Injured Pilots can do a lot of damage. Expecting to see a more of BBBBZ, TIE swarms, or Bug Zappers, or fat pancakes? The new deck will do a lot more for you.
In tactical terms, it's like giving targeting priorities to your pilots. Compared to FFGs other games, it's akin to setting your agendas in Imperial Assault or your scenario in Armada.