OK, there are two ways I think Intelligence can be modelled:
1) You have a Foreign Affairs budget, money allocated to this budget has several key functions:
(i) How many diplomatic contacts you can make each turn.
(ii) How quickly your international reputation repairs after it drops (and how badly it drops when it is harmed).
(iii) How much your Intelligence points are boosted by, as well as how quickly your spies 'advance'.
(iv) Boosts the rate of cultural transmission to other nations-whether passive, semi-passive and active.
(v) Pays the cost of spy units, embassies and Intelligence Improvements.
How much money you can allocate to foreign affairs is effected by your level of Isolationism (a social engineering setting).
2) You build 'spy' units but, unlike in Civ2, you don't move them-they instead end up in your national 'Intelligence Pool'. Each 'spy unit' costs money from your foreign affairs budget (and, if insufficient funds have been provided, then any excess units will be disbanded)-as well as a part of the building city's population. Each 'spy unit' grants a base number of Intelligence Points-based on the average experience level and tech level.
3) As you succeed in particular forms of missions, the number of points you get in that mission type is increased (i.e. instead of 10% of 300 points giving you 30 points in Commercial sabotage, frequent success in these missions might grant you 36 points instead-without needing to increase your % allocation). Success in missions also gives XP's for advancing the average 'level' of your spies which, in turn, boosts the number of IP's you get per spy unit.
4) Certain Small Wonders and improvements also boost IP's, give bonuses in certain mission types and/or increases the improvement rate of your spies.
The second model is much the same as the first, except that instead of building spies, you merely 'convert' a part of your population into spies/agents (much as you do with entertainers and tax collectors). Again, though, how many IP's each agent gives you depends on their tech level and 'experience'.
Anyway, hope that makes sense.
Yours,
Aussie_Lurker.