Disclaimer: this idea is drastic. it also wont have much effect until boarding is added.
The core of this idea is to make money a commodity, like batteries and ammo, instead of an all encompassing account, like FTL fuel. here is some specific changes that would need to happen:
each ship would need a unique identifier. you would need this so when you transfer fund from one ship to another, you know which ship if giving the money, and which is receiving.
you would need to add a way to store money. I was thinking in the control rooms, or in a new part called a vault
you would need a way for players to get money without boarding a ship and raiding the control room. perhaps the control room could be dropped when it brakes, and players could pick it up with a tractor beam or something.
some advantage of having vaults. maybe higher health, or they don't drop when destroyed, meaning you have to send crew onboard to get the cash.
now that the changes in how money is spent.
in order to upgrade a ship you would need to have the funds on board.
when buying a new ship you could choose to either take the money for one ship, or split the cost between all this ships in the system.
you would not be able to spend money that isn't based on a ship in your system.
I feel this would add more reality to the game. a static base would have more of an advantage. you could store funds without the rest of an enemy stealing it. this would also add a new class of ship: transport.
please let me know what you think below