A bold statement I know and probably haven't spent enough time thinking it through but hey here it is anyway. Just thought it might add an extra layer of tactical options/restrictions
Thought it might be nice if antimatter was a depleteable ship consumable no regen.
How would this work ? Planets would manufacture antimatter through an orbital structure. Antimatter tanks would be needed to hold (fleet sized) quantities. extra production facilities increase production rate. extra store tank increase max supply held at planet. Ships would then need to get within its supply sphere range to be re-fueled (similar to a repair station transfer).
Effects on fleets
Hard version
Every ship has antimatter fuel tanks (which can be made bigger through research) antimatter cost for abilities/travel is reduced from current. Ships can become stranded if they don't leave enough fuel for the trip home (have an optional Bingo Fuel, safeguard which can be turned on or off)
Introduce 3 Tanker ships one from each class. They would carry large antimatter tanks and be able to ranged transfer refuel a fleet and thus extend its jump range and or combat power longevity.
Passive ability tankers which are destroyed with more than 50% full tank have a large area effect explosion from the matter/antimatter reaction when containment is lost upon destruction viable suicide tactic and also a good way to cripple your own fleet if you keep your tanker to close to other ships.
Would create the need for tanker supply lines for deep large fleet assaults, although extended range small fleet hit and run would just require a tanker to come along. Capital tankers could possibly use trade ships to re-supply them as a secondary source of fuel.
Advantage to defenders as the will have greater and longer use of powers.
Crippling tactic, destroy a planets antimatter storage tanks and set you enemy back several minutes/hours of production making it harder to launch attacks on you, hit and run tactic more viable as a defensive measure.
Soft Version
Ship Jumps normally use antimatter but can also use a "general emergency jump capacitor" which uses no antimatter and will allow the ship 1 jump or all the way back to the nearest antimatter facility.