If the ship says "hey boss, that's beyond our maximum range" but you decide to try and fly to Andromeda anyways, its your own fault!
That said, consider a system for SE5 in which you have:
- Capacitors (supply storage)
- Fuel tanks (ordnance storage)
- Reactors (scripted)
Each turn, the script will check the storage levels on each ship and convert fuel to energy based on the number and level of your reactors.
Various power and efficiency ratings are possible, of course.
Flying or fighting too long without a break would drain your capacitors until you start taking out of supply penalties. Resupply depots would provide ordnance/fuel, while all facilities could provide some amount of supplies/energy to passing ships.
System defense ships would max out on cheap energy storage, since they have lots of places to recharge from. Scouts would go with just enough storage and reactors for a turn's worth of movement, and carry lots and lots of fuel for the long hauls.