One problem that was mentioned with regards to the damage deck ruling was that players could, to some degree, control the kinds of criticals their ships receive. The crits can be 'tailored', as it were. I would add (don't know if this was mentioned) that the old deck is somewhat 'safer' and will usually be chosen, even though the new one is better in terms of general gameplay. What's the point of introducing a new deck if it is not used?
My proposed solution is very simple: each player's damage deck will be used by the opponent during the game. So you (slightly) control what criticals the opponent gets, rather than what you get. This matters of course for squads that rely on criticals (Etahn, Ten Numb, Saboteur, etc.) but will generally encourage use of the new deck in many cases. In fact, I don't think anyone will choose the old unless he doesn't own the new one. This makes it possible to maintain that the old deck is still legal, but stimulates use of the new.