Obvious idea for new Intel projec: "Set bugs". Targeted against enemy ships. Kind of minor Version of Crew Insurrection - you can see the ship path, observe system it passes, cargo, build queue (in case of SY), but you can't actually control ship. I think it's much more interesting than dull Crew Insurrection. Main feature is that enemy is not aware that this ship is a spy.
Or else, make it Advanced Crew Insurrection - crew is yours, but pretend to be loyal to previous master. They follow his orders, but you can cancel them anytime and take full control over ship.
Same for planets (Adv. PPP).
I remember someone else requested something similar somewhere, but I'm not completely sure
Anyway 2 request mean that it's a popular wish, isn't it?