It seems like you could just make the smaller ones much slower, that is to say slower than their relative size would suggest.
Forgive me, but this is not in agreeement with what Steve is after, I think.
It seems to me that with the refueling changes, Steve wants to introduct a new layer of complexity in the game. Basically, refueling now becomes a serious logistic concern, instead of just a "magic fuel transfer" between ships as it is now. And so, tankers and the new refueling stations become an important part of projecting power in space.
No longer you can just dump fuel on planets and refuel there, or just transfer fuel between ships. You now need a specific infrastructure in order to do that, and so you need dedicated tankers or forwards bases (the refueling stations). I personally like it, though I can understand why some may not,
But if this system is applied, and it seems to me it will be, then it is not advisable, and should not even be possible in fact, to have a small and cheap refueling system on every ship. No matter how slow it is at transferring fuel, it would defeat the entire point of this new system of refueling. What does it matter if it is slow, if you can just slap it on every ship? You may as well just do away with it.
And this is why I think 500 tons is a good size for this system. You don't put something like this on every ship, just on ships you want to have it on. And it seems to me this is exactly what Steve wants to achieve with this change.