In my actual game, there is an assassination loop.
An other empire constanly get their leader killed :
20 death in less than 10 min at 4X time.

Same with a sabotage loop.

A similar solution to the empire reputation :

A spy is detected stealing tech -> tech stealing to that empire become way ...

Counter intelligence is weak now. I didn't see any change between going full mission and half mission half counter. Still lose stations and didn't catch a spy.

The intelligence gameplay is too isolated from the rest of the game.

It doesn't take into account the distance to the target, the tech level of our and the target empire and the species.
There is also no events for intelligence like those for exploration.

First part, the distance :

It's illogic ...