Consumables work to a limited degree but they are random and can cause issues if there's power involved (the old Hunter ammo in WoW is a good example, or the tech 2/faction ammo of EVE.) Directly purchasing more damage basically raises the bar for everyone, making those with money more powerful whilst those without are left disadvantaged and ultimately leave.
Money-sinks, again unpredictable and more often than not ineffective. It requires the item being sold to be worth the cost e.g. more power, which leads to the previous issue. Or a more familiar scenario, the suggestion that caps should be locked to official factions, same deal just replace factions and caps with money sink and large amount of credits.
Fees on the otherhand are consistent and predictable (depending on the type) but they are hardly money sucking vampires and can potentially put players off if they feel they must grind to play.
I'm no economic expert, but like you folks I've played my fair share of games and seen the systems at work with the best ones hardly being noticed, we all buy ammo and bots/bats without thinking after all, along with fuel for cloaks and jumpdrives. The trouble is the systems we have hardly make a dent in the majority of pockets when compared to the potential income which leads to a surplus of credits and stagnation.
Personally I'd prefer a cost for Jumpgates and docking with upkeep depending upon ship size/power, nothing huge, maybe 200 credits per ring dock, 1k for mooring and Jumpgates. Ship wise 20k a week base for fighters light to meds and upwards of maybe 300k for large transports and caps? It'd need to be ironed out but you get the idea.