Instead of just adding an extra "0" in their damage stats, add actual abilities like;

"Assimilation Protocol" - like Boarding Party but it will turn the target ship into an NPC ship (like a Sphere).

"Selective Sensor Exclusion" - like Scramble Sensors but renders all Borg ships invisible to the target instead.

"Tactical Vector Adjustment" - like Abandon Ship but (for Cubes) instead of just self destructing it will eject a Sphere with upgraded Sphere stats.
Spheres will eject Probes and Probes will eject Odysseys

Stuff like that.