The fast missile launcher already hits most of the sweetspots for fuel/speed/reload/whatever. It’s an excellent weapon in the 600-700m range, and can comfortably be used in many less optimal situations with a painter. Use those for now.
Changing the missile fire behavior would be a significant balancing headache. Some of the missile systems are already very good, you’d have to nerf them to hell and back in order to make them fair using their optimal firing time.
However, since the fuel is based on travel distance, it is almost a double penalty for the slow missiles. A fast missile takes a little over four seconds to sputter out, while a missed megaton looks like it takes somewhere around eighteen. The enemy would be doing you a favor by shooting down your missiles at that point.
I think it’s interesting that there’s a feedback loop with missiles and hitting, as it really puts the target painters into play. The dichotomy of the slower missiles is pretty severe though. The megaton in particular is so slow that the optimal DPS achieved for it is just outside of minimum range, and the max range on the weapon is the lowest of all the cruiser missile/rocket solutions. Players (if they use it at all) are using it for short range attacks… it does not need to have the highest fuel load in the game.