[Roanon]

Having a (low) chance of success is a very good idea. With these lesser chances, the ability to store counterintel points should be removed, and the system might actually work. You either have more CI or you don't. If you do not have enough CI, the spies do not make devastating damage for sure every turn, but have a small chance every turn. And this not after dozens of turns wearing down CI defenses but from the first turn of the intel clash onwards.
Another interesting option might be to offer different spcialized CI projects, which are more effective in their field (e.g. planet sabotage, ship sabotage, etc) but do not affect intel in other fields at all. So you have more choices than just "everything to counter intel" every turn.