There is another thing I had in mind about intel. Since finishing counter-ops opens screen for enemy intel, maybe counter-ops shouldn't be ever finished (make them cost endless amount of points).
Also IIRC the number of counter-ops going on in the same time is important, so making counter espionage a seperate process would require to change how the whole inter works. Maybe just making counter-ops a never-finish project could be more easaly implemented than changing the way the whole counter intel works.
I'd like to see a slider system, where you just drag over the bar to set a proportion of Intel Points to be put towards Counter-Intel. Also, if you aren't running any offensive projects, the points should be automatically put towards defense.