Sounds great, but some small suggestions (mostly cribbed from Endless Space 2's ground combat system):
1. A max invasion cap that can be modified by ship types (troop transports/siege?), modules, skills.
This limits the amount of just "oh i'll raid today, swap out the spare guns, sell all the trash and AI cores from our last run and load up the gun totting hobos we keep in storage". Fleet composition will actually matter more for serious raids. No showing up with a cruiser and 4 atlas' full of marines and expecting a quick and easy victory.
Marines use crew quarters, not storage. So most ships aren't able to carry large numbers of marines. The ship that is built for raids, the Valkyrie, can carry a lot of crew.
Maybe Pirates should get some not quite Valkyrie ship for their raids? A modified Cerberus could fit nicely.