Will we have a base or a permanent place we can upgrade ? I think you said something about the sub being the base and bringing some bonuses based on its installed techs. One of the success factor of these kind of games is the sense of parallel progression (characters + something else) and having a base to develop as you go on campaign is certainly a big part of this factor.
You could "build" your subs, with quarters (more total perma crew to pick from to build the dream team for each mission), tech bench (research or refactoring to improve loots), training (idle members still get some XP even if not in mission), tankers (more fuel to stock), engineering room (less fuel consuption when moving), negociation table (better prices on market), and so on.
On missions, you could have sub's parts to retrieve, or engi to free/capture and offer/force them to work to improve the sub, special shop with more or less rare pieces of crap for the sub, etc.