[PvK]

Well generally they are for getting the AIs to design units and planets in ways other than the way they otherwise would. Want a ship with more that two types of weapons on it? Want to have a mod where the AI doesn't over-use certain very expensive components or facilities? Want the AI to build a specific ship design? Well, these give you more ways to specify to an AI what to do.

It's too bad they are limited numbers and not unlimited names, but generally it makes sense to assign meanings to them and use them accordingly. For instance, you could have ability 1 mean "cheapest engine" and ability 2 mean "most cost effective weapon" and ability 3 mean "shields to use".

Without modding abilities, Ion Engine I, II, III could all get ability 1 - it would be true throughout the research path. The Phased Polaron weapons could have ability 2 on levels I and II of that weapon, and then maybe again on level V, or VI, depending on your opinion. The shield techs could all have ability 3 except for the levels of phased shield that you consider too weak to use. Then in the AI designs that use these, instead of asking for shields, you'd ask for ability 3. Warships might ask for engines, while transports and colony ships, to be cost-effective, ask for ability 1 instead, etc.

PvK