Nerf the amount of power gained by singularity cores, but remove power penalty.
Miracle Worker needs some work while most of it still works well, there are some big outliers.
Give romulan cruisers cruiser commands, now that we have vanguard ships that still get cruiser commands there is no reason for this inconsistency.
Give all fed ships without cloak Sensor Analysis and give fed science ships a upgraded version(double the stack maximum and gain rate).
Give all carriers except flight deck carriers the vanguard mechanic , vanguard carriers could use warships or attack ships instead of raiders increase throughput.
Give cruisers a unique gear option would make a good reward like new pets, experimental weapons and secondary deflectors.
Cloaking revamp: cloak should just work like battle cloak, battle cloak should work like enhanced cloak, enhanced cloak should work like the scimitar console attack while cloaked. Just make the scimitar console give enhanced cloak. I have hard time believing that tech died with the scimitar, but the b'rel enhanced cloak has stayed strong. I also believe standard cloak is just not interesting.
T1-T5 enhanced versions(passive stat buffs) of these consoles for dilithium.
Revamp armor system with light medium and heavy armor options so you can tune harder content better, make engi armor consoles to just set HP buffs. Remove/nerf BOFF resistances. Light could favor defense with increased miss chance or a dodge chance? Limit what ships can't equip this with maybe light cruisers being the only engi class ship able to. medium could just add moderate amount of resistance , heavy could be the highest resistance and be restricted to the largest of ships, cruisers, carriers,dreadnoughts,juggernauts etc.
Destroyers lets make these ships into the Tactical/engineer ship version of the science destroyer. Switching between commander engi and tactical, cruiser commands and experimental weapon.
Revamp command spec tree to focus more on team support and pets. Example: like making the torp expose team wide for _ seconds. Remove the exp bonuses and other bonuses there and make them better pet/team support bonuses.
Bonus: A new specialization either dealing with pets or heavy weapons torps, expermental weapons, mines.