This is VERY similar to what I suggested above (my own variant of the BotF model

!) In mine, though, the success chance, frequency and sophistication of intelligence operations was related to tech level, funding AND # of 'intelligence improvements', specialists and Wonders-all of which contributed to your 'Intelligence Point' pool (though I concur with you, S_S, on the possible role of culture flow as well). You then determined what PERCENTAGE of your IP's you want to devote to different types of intelligence activities.
(a) First up, you decide what % of your IP's you devote to Espionage (spying), Sabotage and Counterintelligence (defence against foreign intelligence missions).
(b) You then FURTHER decide what % of the points from (a) you wish to devote to each nation you are in contact with.
(c) Lastly, you can then further split your IP's up, on a % basis, into domestic/civil; Military; Scientific; Industrial or Commercial. If you don't allocate any points at this level, then the computer will simply attempt each mission type on an equal basis.
As an example, lets say that you are currently generating 600 Intelligence points every turn. You decide to allocate 40% (240 points) into Espionage, 20% (or 120 points) into Sabotage and 40% (or 240 points) into Counterintelligence.
You are currently in contact with 4 civilization-the Romans, the Babylonians, the English and the Egyptians. You are currently already at war with Babylon, so do not decide to devote too many resources to them-allocating just 10% of your IP resources to this nation (24 points, 12 points and 24 points respectively). You are allied to England, and so only devote 10% of your resources to them too. Egypt you are not too sure about, so you decide to devote around 30% of your resources to (72, 36 and 72 points). Rome, though, you are DEEPLY suspicious of (having only just come out of a war with them). So you devote 50% of your total resources on intelligence operations on them (120, 60 and 120 points respectively). This essentially means that your intelligence missions will be most succesful (and most frequent) against Rome, though this might change if they have allocated significantly more IP's into counterintelligence!
Lastly, you could divide your IP's up even further. So, for instance, if you wanted to really learn about, and HURT, Romes economy, then you might devote 60% of these IP's into Economic-which amounts to 50 points and 22 points devoted to Economic espionage and Sabotage respectively! This would give you information on what kind, and how much, of certain resources Rome possesses, what kind of economic improvements/wonders they have and who they are trading with-and for what. It would also give you a chance of damaging, destroying said improvements, cutting them off from their resources and causing some form of disruption to their trade routes!!
Information on successful (or very unsuccessful) Intelligence Operations would be given in your 'pre-turn' summary list-under the 'Intelligence' heading!
Aside from this, if you have an opportunity to comit an especially vile attack (such as terrorism, assassination or the like) or plant evidence implicating another nation (via your counterintelligence) then this will appear in a pop-up as a yes/no option. All other missions, however, will be performed automatically. For example, lets say that you learn of a Roman 'Economic Great Leader', whom they are using to boost the wealth of their cities. At the start of your turn, a pop-up featuring your 'spy-chief' comes up, saying you have an opportunity to assassinate this leader, and if you want to do it (with a standard warning about your reputation

!) If you click 'Yes', then a further message might come up asking if you wish to try and implicate another nation in the assassination attempt, with each button relating to a VIABLE nation. You decide to cause trouble, and Click on Babylon. Thus, if you were successful, Rome's Counterintelligence would detect evidence implicating a Babylonian spy in the murder of their Chief Economist-which might lead to WAR

!
Yours,
Aussie_Lurker.