I like intel projects. I like to decide if I will ruin a planet, kill population, or just spy on the empire's designs. I sure wish tech stealing was wor useful.
I realize the intel projects is a little hokey. I would like it if counter intel was automatic based on number of facilities or something.
One thing I never understood in any 4X game (and by that I mean SE3, SE4 and GalCiv/OS2

), is how just building intel facilities gets you intelligence points.
Would US CIA be better if there were more CIA buildings nationwide? Not really, what works is sources in the field. IMHO, intel should be improved by building facilities near the empire you're spying on, not a megopolis near your home planet.