Hows this?
Intel points are generated empire wide, as per. They can be spent on "general" stuff (projects etc), either offensively or defensively, or to purchase "agents" (who are VERY expensive)
"General" use would represent surveillance, signal intercepts, watching the news (all the things that modern Intel agencies do, essentially), and the use of low level agents. Certain mission types (especially offensive ones) would be unavailable. You can assign your "general" points into a number of pools, on a per race basis, or into the defensive pool (this is borrowing heavily from the Star Trek 4x game).
Obviously, you can only assign offensive points to races you have "met" (probably a good measure would be to have detected at least 1 of their planets with your own ships, not just having seen their ships).
The "offensive" categories could break down into ship based (steal design, plant bomb, crew insurrection etc), planet based (plague bombs, planet stats, sabotage build queue, destroy facility etc), research (steal research, sabotage research), intel (steal intel, sabotage intel, identify agent, double agent!!), etc, etc. You build up points until a randomly triggered "project" is generayed. Then, your existing intel pool is measured, used and reset. You don't know what effect you'll get (most intel is about taking opportunities, not deciding what you want). You can decide how to bias your activities, but nothing is certain.
Obviously, the more points you assign per race / Category, the better you'll do. The points accumulate turn by turn, until (randomly) a mission window appears, and they convert into an actual effect. This should be random, but time linked, say a 3% chance of a mission per turn (this can be fiddled with, 7%/turn for the first 5 turns, then 4%/turn for 6 turns, then 3% turn, until a trigger is generated). This makes missions random, but not stupidly so. Any unassigned points the race has stay as Counter intel, and are applied against ops running at you (so you must make a choice; do I run ops, or defend myself?)
Op Example: you push 1000 points / turn into "ship effects" on the Terrans. After 5 turns, a trigger pops up, and you "convert" your intel. You've been inputting 1000/turn, so have 5k built up. The Terrans are putting 200 turn into counter intel, so your total pool is 4k (200x5=1000, 5000-1000=4000).
4k on "ship effects" gives you a range of possible effects, steal ship design (30% to choose, 60% base success), plant bomb (10% to choose, 20% base success), sabotage engine (10% to choose, 20% base success), drain supplies (30% to choose, 60% base success), misdirect movement orders (20% to choose, 40% base success). One is selected at random (%age chances can be assigned for a given pool total), then success / failure determined. If a bigger effect is chosen, chances of success decrease, but the benefits are greater.
Overall, this means that you can only CONSISITENTLY pull off big scores against races that you are targetting hard, and that aren't big on CI (but those who ARE big on CI don't really have enough points spare to runs ops at others), unless you are massively superior in intelligence, in which case its realistic anyway.
Agents : add a new planet facility (1 per system - agents are rare), Intel Complex, that permits you to run 1 agent. You don't get him for free, you have to buy him. This is an alternative use for Intel points. Once you have at least 1 unused Intel Complex, a new "race" appears in your intel screen. You then apply points there as normal. After so many have accumulated, you have a brand new agent! You can still apply points to certain areas, but that now represents training in that area, not an operation.
Agents have skill %ages in many areas, related to the intel cats. As they survive missions, or train, their %ages increase (training will have maximums in rate of gain and a %age cap, to encourage giving your agents real world experience). The major benefit of agents is that they can CHOOSE their mission type and race (and have some extra missions available that only they can do). Obviousy, their skills affect their success and survival chances.
If an agent is caught / killed, you can begin recruiting a new agent. If you have 3 Complexes, and 3 agents, and a planet containing 1 of your complexes gets glassed or captured, you lose an agent (gets cut off from Control, and disappears)... If you had 4 Complexes and 3 agents, that would eb a different story
Obviously, a very large empire could own MANY systems, so maybe a hard limit of 10 agents should be put in. You can have more Complexes, so territorial losses won't necessarily blitz your agent corps, but after a while the micromanagement gets nightmarish, and to be honest, NO government is keen on having too many top class spies wandering around.. Its just ASKING for trouble
Agents can be assigned to CI too, but would ONLY apply to a particular planet / ship (if you happen to know or suspect that another agent is being used against you in a very specific location say, or you want to protect the RD in a given strategic system to protect your fleet supply line - I think agents should be mostly offensive, James Bond stuff. CI should just be background usually)