I'd like to see the cost of hiring and paying crew increase. I suggest that crew purchases increase to 200C, and their monthly pay to 100C (this is what I've been playing with recently, and it may be a little too high, but it certainly makes the changes felt).
This has two main effects:
1) Running Costs: "upping" your fleet size is a much harder decision. You have to think much more carefully about whether that new destroyer is worth the running costs, or whether you can afford to invest in a cruiser. It's harder for ships to earn their place in your fleet, which I really enjoy. Investing in Efficiency Overhaul is a more attractive prospect, since it cuts your salary bill by 20%.
2) Losing crew is meaningful. A ship that goes down with all hands could cost you tens of thousands in crew alone. Therefore, Reinforced Bulkheads, Blast Doors, and other life-preserving effects become way more valuable. Since the same crew also pilot your strike craft, it makes spamming these a far less attractive option, too, and incentivises mods/perks/LPCs that keep casualties low.
On a related note, I would also significantly increase the cost of officers. 5,000 base, +1,000 per level. This means you only ever take perks if they're the ones you want. Currently you can just pick up a bunch of "whatever" perks. Some officers will hit a "skill ceiling" where the perks available to them just aren't ones you're willing to pay for. It's interesting to have officers who don't all hit level 20 eventually.