A need for Materials might actually make it less common practice. So a price set based on distance and size of ship, but then also a materials price maybe set based on extent of modification. One might go to, say, Farseer, then and instantly summon the Beluga one just bought at Founders World. Then after modding it fully, one might stare horrified at the amount of rare mats needed to get it instantly transferred to anywhere else.
Of course, people might just consider it a wall in the way of their fun times, another grind just to keep them from having maximum fun all the time. It would, though, be nice if something could stay a time-sink to achieve: Remember how much effort it took to get the Thargoid mission in First Encounters, and how exciting it was to finally get there...
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Require mats for transfer? You could do. Like you say, it's adding a bit of grind to the cost. Would make it less desirable to abuse. It still doesn't fix the sense of realism, though.
If anything, I'd love for FD to implement more minor delays - not make things instant. When I lose concentration out in space and fry myself near a star, I sit and wait and watch little counters as the AFM gradually repairs my modules. Why can't this same simple mechanic be applied to station repairs... and restocks... and cargo transfers?
Sorry for going slightly off-topic again. I just don't see the need for things to be "instant". I mean, if this has been done to facilitate different types of gameplay? I made the trip out to Sag A* via Jaques. It was great and I'll slowly make my way back when I can squeeze in the time. But if I suddenly feel the urge to join in some combat (with that account) I don't get the option to instantly transfer myself back to the bubble. I made a choice, I'm following it through. If you're running trade runs in your T9 and you suddenly feel the urge to join in a combat zone, why does that absolve you of the responsibility of your choices? Finish your trade, go get your ship, and then join in the combat.