Console Powers inherently break the opportunity cost balance of Bridge Officer Powers. This creates unexpected and often undesirable synergies, like the ability to stack more energy drain sources that will overpower any ship's ability to deal with it.
It also comes with a drawback for each power individually - their cooldowns tend to be long so that the problem is diminished - but that doesn't really help the issue, since it often only matters in PvP that you can do something at all ,not how often you can do it. On the other hand, if you don't use these synergies, it makes these powers feel irrelevant - if you can use an ability only every 2 minutes but can kill a PvE enemy within 50 seconds, you do not only not need this power - you can't even work it in your "PAWN-THE-AI" power rotation.
Solution 1 (Simple) - Making all Console Powers Devices
The simple approach for me that solves at least some of the opportunity cost issues is to make all consoles devices. That means they have an opportunity cost with batteries and some of the new consumable items introduced with FEs and missions.
This change would probably require adding device slots to all ships that have less than 4, otherwise Cruisers would have an unfair advantage.
Solution 2 (Complex) - Turn all Console Powers into Trainable Bridge OFficer Powers
This basically solves all the opportunity cost problems. Question is how to implement this. The technical nitty-gritty stuff would probably be complex, but I can't say anything on that. From the player side of view, I could see the following happening:
The consoles remain consoles, but they do no longer grant a power, but instead some kind of non-standard bonuses comparable to other consoles, with the extra perk of being universal, so you can slot them where you normally cannot get such a bonus. (Examples: The Ablative Armor Generator console for example could simply be an Ablative Armor console that you can slot anywhere. The Theta Vent console becomes a console that boosts engine power or maybe the Starship Engine Performance skill. And so on)
The Consoles also gain a new option - a "Train" option. This represents training a Bridge Officer to get the most out of the console. Training the BO gives him the old console power as regular BO power. The powers cooldown could be altered so that it works better in the context of a regular BO power, taking into account that raising a BOs rank in a console power reduces the cooldown.
A further perk of this is that it solves a certain conundrum with the existing ship system - the "felt" BO slot diversity would considerably increased if there are some new powers that you can train - even more so should these powers have no "class" affinity and any console power can be taught to a BO. (THough I leave it open at this time whether that should happen).