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Makinus said:
you can also mod all ships as units (fighters for example)... but i�m not sure what this would do to the AI....
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Fighters are unable to travel through wormholes, and drones have a limited set of orders, so it won't really work. That, and there are a few other significant differences between units and ships: units do not require maintenance (it should be possible to give them a reverse resource creation ability though), units do not have ship experience, and they do not take partial damage.
So you will need to keep at least some ships, if only to carry the fighters from one system to another. The Highliner mod does something to that effect, by making real ships *expensive*, and by increasing the cost and firepower of the fighters. In this mod, small fighters are the rough equivalent of Frigates, and the biggest ones are Light Cruiser (if memory serves).