I have for a while thought about more granular HQ permit points, as I said back in ‘21: Some thoughts about HQ Upgrades, Base Permits and Base Expansions - #5 by McCowen . The idea would also be that ships require permit points (based on size/cost), and base size is more flexible but larger bases provide diminishing returns on HQ points spent.
In terms of storage, I think a few more storage buildings would help, a 5 area one, a weight one, and a volume one. It’s been suggested to use ship components to have truly massive storage buildings: More STO buildings .