1. First idea would be to rebalance the temporary upgrades.
Consider that for 400XP you get 3 ships, fully equipped. One is always the 3 turret tough/fast one worth about 8000 scrap, and the 2 smaller are worth about 8000 combined. So 16k worth of scrap AND instantly built for 400XP, vs 2000 scrap for 200XP? Sign me up! Granted, you don't get quite what you want, but still...its a lot of value. It probably needs to be slightly increased to 500XP.
50 RPs does not have much effect on the game and at 200 XP is way overpriced. Having a few tiers of this to give 100,200,400 RPs at the cost of 100,200,400 XP seems reasonable. This would allow people to start with more advanced tech, at a price. You can use the same button even... clickable up to 3 times with increasing rewards/costs.
Similarly, 2000 Scrap is not very much to work with for what? 200 XP?
Having 3 tiers of bonus cash would be an idea as per above. I'd say 75XP/150/300 for 2000/4000/8000 scrap?
The smaller ships reinforcements are a bit pricey at 300XP. Considering their value is less than half of the bigger reinforcements, I'd drop their price to 250XP.
2) Secondly, you can have permanent upgrades that give minor bonuses to your gameplay.
Example, for say 1000XP you could unlock Quartermaster, which adds +2 dudes to your starting lineup. Thats 2 extra pilots, marines, whatever.
Just about any variable could be done in this way: Procurement Expert for +500 starting Scrap. Brainiac for +5 RPs starting. Even stuff like 2000XP Master Tactician for 5% speed boost. WeaponMaster for 5% more damage. Lots of obvious possibilities.
3) Moar Tech. I have an entire long wall of text based on pretty conservative ideas for ways to implement lots of unlockable weapons, some usable early (tractor beam), some unlock new tech trees.
4) I do like the idea of permanent saving of captured UNMODIFIED ships/stations for the campaign duration. :-) Adds a nice gacha feel, even though I doubt its all that powerful. What would be powerful if you were able to mod them and cherry pick advanced guns, then perma-save. That would be too strong. Thus, you would disable saving an alien vessel if you modify it. Or disallow mods (seems worse).