It seems like I wasn't too clear as well, no wonder now that I look back on my Posts.
I didn't advocate setting up a really... how to put that... detailed intelligence system, but rather adding agents to perform the tasks. The other areas you mentioned (that is, geographical areas or the need for ships) wouldn't work in a game with such a scale as Space Empires. The same could apply to my suggestion as well obviously. So I will try to develop a bit what I have in mind when I speak of making operatives into the game.
You would have to "recruit" these agents by spending these intelligence points, which will remain as a very convenient abstraction. Then you would have to train these agents, by spending the same points, or you might send them to enemy systems for "learning the hard way". Obviously, all projects will cost intelligence points, so you would have to choice where to spend the points. And then you could consider giving the agents basic abilities, something along the lines of "Counter-Intelligence, Spying/Sabotage and Loyalty/Combat" (That is, defence, offence and escape)
As this may (or may not, I guess it depends on your own taste) be too complicated, why not adding some training program to improve the efficiency of either (both?) offence and defence projects? The point would be to give something else than Counter-Intelligence to plan when Intelligence isn't needed. As for now you will put your points into Counter-Intelligence when you cannot do anything better with these. It might be a bit different if you actually had to spend Intelligence points to improve the efficiency of your projects, or even to gain access to new projects.
It is only a random idea, but I would definitively like to have a choice between CI and something else when you don't have to try your luck at launching a few projects. For now choosing CI in such circumstances is usually a no-brainer, unless you are actually plotting to send a few operatives all at once against a single enemy in three years or so.
Who knows with all these scheming minds around?