I wonder if this ever been suggested. But Ill post anyways...
Since raids and invasions are a bit odd for now, my idea is to have an extra equipment category.
Call it "troops" and what not. It will allow you to equip groups of soldiers, COs and special units we get from missions and raids.

One idea to consider is to have another research or resource tab called "academy" Where we get some points to spend on troops the same way we do on research or artifacts possibly accumulated from planetary structures. Researching troops will grant access to higher tier soldier modules. They will come in packs as a module. Example: basic scout x5, advanced vanguard x50, elite rifleman x 100 etc...
Your soldiers would give you invasion stats aswell as invasion-defensive stats if you are on guard all depending on the type of troops you have.

Another idea is to have them equippable separate from ship decks. Maybe mirror the shipdecks in a secondary value or have it be governed strictly by ship size.

What got me thinking about this is the Genetarr Matriarch missions. It would be nice to have her as an ally. So doing such a mission would allow for a special co or soldier module. Maybe some crews would allow for special power such as extra pvp or npc slot or scanning bonus. -The Matriarch would of been perfect for that...

i already posted this

viewtopic.php?f=6&t=2960

glad to see more ppl are on board with it! only got one reply to it.

OOh! sorry...
I love your Idea of having quarters and hangars! That kinda solves it >_<
Aswel as NPC controlled planets!