Currently, a fuel cell is worth 50 fuel, but you cannot refuel a machine if it's just over 50 because it'd waste a fuel cell, which means high fuel-cell usage batches cannot be processed most of the time. I have an idea below that would not change how much fuel cells are worth, but would make them more flexible:
Make fuel cells worth only 1 unit, but make it so we can make 500 of them at a time. Make em stack at 500 in our inventory. Then whenever we refuel, it'll always be able to refuel to 100, assuming we had enough fuel cells in our inventory. It'd literally be the same as it is now, except more flexible!
* 1 fuel cell worth 50 units each becomes 50 fuel cells worth 1 unit each.
* 10 fuel cells which would total 500 fuel, becomes 500 fuel cells totalling 500 fuel.
* Stacking 500 fuel cells would be the same in this change, as stacking 10 fuel cells right now.
I'm not sure how you'd do the recipe though. Maybe lock the amount you create in 50 unit increments.