Yea, I don't want infinitely-farmable stuff to give XP. I'm ok with temporarily-farmable stuff (nebula ships) giving XP as long as the scenario progresses towards termination or there's some sufficient motive to finish the scenario; that's true for the 3rd one (and the 4th one, which is basically done now, just gotta do some other stuff before a release), but the 1st and 2nd need work.
For AI ships, I'm thinking having them give 1 point (per mark, perhaps) of shadow-charge might be a good way of having them give something, but not something that can be infinitely farmed. Even that may prove unbalancing by letting the champion drop truckloads of projected ability units onto the field in the middle of a massive attack. On the other hand, "in the middle of a massive attack" may be exactly when they need to do so. On the third hand, it might lead to a lot of having to pause to properly use the abilities (even with better keybinds for using them) before your capacitor maxes out from the AI ship deaths, etc.
Lotsa hands to consider.