Simple answer: Cryptic is not going to design a section of the game that restricts its players from using the things they've won in lockboxes or bought on the C-Store as it creates an area that devalues your purchases and creates an in-game reason to not spend money on the game.
I, too, would like to see something done about the consoles as many of them are both extremely unfun to play against and are very powerful with far less opportunity cost than their bridge officer power equivalents. In at least two cases (Graviton Pulse Generator and Anti-Matter Spread, as mentioned above) they are markedly *more* powerful than any of their analogous bridge officer powers.
Try fighting a team where everyone has cmdr lvl tac and sci powers, now thats stupid. Fortunately the queues seem mostly clean, only one fight I had was really crazy. Near constant TBR, VM spam combined with CRF and mine patterns...
But in the end I have to say I had some really nice games recently, despite consoles, bugs and everything.