You know that old gag about genius ideas coming to you in the shower? I was in the shower about fifteen minutes ago and an idea showed up.
Everybody has all these ideas on how the game should be updated so that they can fly their favorite lower tier ship at higher level, I'm right among them, and suddenly it came to me to use the console slots for upgrades. Think of it: instead of monotanium armor or hazard emitters you add a engineering or science BO power expansion slot or a "control package" for an additional weapon.
It's a trade off in that you loose that slot from a movement or weapon damage enhancement, etc., but you gain the ability to use a higher tiered BO ability or another weapon. Higher tiered ships would also benefit in that you could more BO powers, etc. You could have your Klink ship set to over kill with every slot bristling with weapons but at the same time you would loose the bonuses of adding consoles that would have enhanced your weapon power or damage resistance or your shield's regen power. It would all balance out at the higher levels and still give benefit to higher level players captaining lower level ships.
It would increase ship customization choice and playability without having to modify the existing programming frame work. The devs could release craftable console mods that would do this and also allow for special quest rewards as well.