Allow the federation to retrofit a cloaking device onto their ships.
In the same way that the USS-Defiant has one, But have the cloaking device take up one of the console slots such as science or engineering.
And make the cloaking device a rare device that is awarded at the end of a long quest chain to obtain one from somewhere.
With the Romuluan star empire in ruins there would be plenty of oppotunities for a federation captain to obtain a Romuluan cloaking device by a variety of ways, perhaps they can salvage one off a wreck and get it repaired or perhaps they could purchase one from a rogue Romulan scientist or engineer after a long quest to track one down, because with an empire in collapse there will be plenty of these around.
This would be the perfect counter, cloaking to balance cloaking.
Does the cloaking device remove several thousand hp from your ships too or is that gonna be left out?