[Q]

I too found intel in the original SE IV unsatisfactory and the counter intel too powerful, especially against AI races with high bonus settings.
Therefore I reduced the effective amount for all counter intel projects to 1: higher counter intel projects can store more points, but are not more effective per point.
Second I reduced the modifier for counter intel in the settings file from 120 to 50. You need now 2 counter intel points to defeat 1 point of an atttacking project.
Third the cost of the more effective intel projects like communication mimic was increased and I added some very costly projects like "planet destruction" (blows up a planet) or "planet infection" (creates a plague on a colony).
And finally I use my intel mod that is included in the SE IV gold CD which makes all attacking intel projects a racial technology. This allows you to create different AI races who will use intel more or less aggressively.
But that's just my personal flavour.