Remember, upkeep is only suggested as an alternative to the current price mechanic where you have to work significantly to obtain larger ships. It can also be flexible, reduce the prices a little - increase running costs a little, reduce prices a lot - increase running costs a lot.
Depending on how much you shift spending from initial spending to continuous spending, you may be helping new players a lot (they get their desired ships faster) and hurt old players (they have to start working to keep using their big ship) or viceversa. However old players can have at leas one advantage, in the form of refunds for credits they already worked for. And you can always park a large ship to stop paying it's running costs.
Tweaking it does not remove the "cheese". It's not really a new game mechanic, either, so I've seen several implementations of it and none of them were really "enticing".
Money sinks mechanics should provide you with actual, tangible advantages (but never "gamebreaking" or "unbalanceable" .. see PowerPlay example above).
There was the "jumprange" discussion some time ago, where we had a pretty nice idea for "fleet management" and "ship moving".
Adding the possibility to have your ship moved by some "moving" company to the station you want it with a -imo- well thought out pricing.
far as I remember:
- slow moving of only your ship for a relatively low amount of money (pilot still needs to fly to the new station somehow)
- slow moving of ship and pilot for a bit higher amount of money (tied to ship value/distance, whatever .. this can be tweaked)
- "instant travel" by basically using the current rebuy functionality (and the refund price, too) in the station you want to have your ship (or actually a "copy" of it, that the station has stored

)
It's totally optional as mechanic, you can still travel as you do now (trading in-game time spent "unproductively" for saving that money).
It gets more compelling, the more money you have, since the single transaction is taking a relatively small toll. (the more ships you have, the more "assets", the more likely you'd use the mechanic instead of spending hours shutteling your ships around the bubble - unless of course you enjoy shutteling - see sentence above)
It allows for instant "emergency" travel (spontanously meeting up with some friends somewhere was brought up frequently and the tedium and timeconsumingness of some of the combatships), at a relatively high cost - kinda the "premium" idea.