Since the powers will not be removed at all, to much time went into developing them.
How about this:
Singularity core behaves just like a warp core power wise.
Remove the innate power penalty from the Romulan ships.
Introduce a science console equipable only on warbirds,
this console provides the jump, warp shadows and quantum absortion.
Do the same with a tac console that provides the singularity overcharge and plasma shockwave.
That way you solve many problems, ships are on equal footing powerwise and people would don't want to use the powers are not penalized for them.
You give the player the choice which power flavor they want to use and get them balanced by having the ship using them giving up console space. Science for defense/fancy powers and tactical for offensive powers. Balancing out defense and offensive from passive consoles with defense and offense from active/singularity powers.
Next would be the battlecloak, from the veteran ship, we know that it is valued at 8% shield and hull.
Canon wise we also know that cloaking devices are rather small and can be carried by normal people.
I would suggest to decouple the cloak from the ship and create devices for them,
Equipping a cloaking device then lowers hull and shield by say 4%, for a battle cloak by 8% and a EBC by 16%.
Could do the same for the klingon ships, after normalizing their hull and shield values and device slots.
And of course turn the fed cloaking consoles into cloaking devices as well.
What is the point of all this? Allowing the players a choice how to equip and play their ship.