There is hardly incentive to use a lot of consoles available to some ships in this game. Particularly when I was grinding for Tier V Starship Mastery, I ended up chucking the ship-specific console. That console tended to be a nuke with a long cooldown for EPG or ControlX that I wasn't specced in, or just a personal or AoE buff that lasted a short time, also with a cooldown. The only ship-specific console set I find myself using is the Flagship Technologies 3-piece, because it feels like a worthy console set with some actually nice bonuses. This was released two years ago, and of all the ships I've stuck with, it was the Odyssey because the consoles are good.
I've also previously owned the Tier 5 Odyssey set. I had to throw out all three of those consoles if I wanted to get some damage output. And again, whenever I used another ship, I stuck to the same mess of good consoles like the Assimilated Module, ZPEC, Quantum Phase Converter, and all the Vulnerability Locators I could stack, then some spare Plasma-Generating Weapon Signature Amplifiers/Nullifiers I had lying around. At no point did I feel compelled to slap on the console that came with the ship.
I just feel like some extra fun and variety could be added to the usual flying and gunning by making these abilities either innate, or
giving them their own console slots separate from the others so as not to interfere with the other slots. Though honestly, I feel like any ship that can separate its saucer should be able to regardless, or activate console weapons, e.g. Point Defence System, Disruptor Autocannon.
Consoles that come from a specific ship, but can be slotted on any ship.
After some deliberation with the other users on this thread, I thought I would change how I would like for this to work. I'm not exactly the best with words, but this is for, right now, the clearest wording on this subject.
Add a dedicated console slot(s) separate from the maximum of the combination of 11 Engineering, Science, and Tactical console slots for all non-Miracle Worker ships, and separate from those 11 slots and the 1 Universal slot on Miracle Worker Ships. This dedicated slot can only be used to seat a specific console that comes from that ship and its variants.
For example, the Exploration Cruiser Refit's exclusive console, [Console - Universal - Antimatter Spread], while it may be usable on any ship, may only be slotted in its dedicated console slot on any Exploration Cruiser or Dreadnought Cruiser variant, to include Exploration Cruiser, Exploration Cruiser Refit, Exploration Cruiser Retrofit, T6 Exploration Cruiser, and all Fleet versions.
Remember kids, the difference between TRIBBLE around and science is writing it down.