[Suicide Junkie]

What about a hybrid system, where you could have a relatively detailed leader, and statistics on the agents in the leader's group?

The leaders could gain experience as they complete missions with their agents (start them out small, doing easy missions) and if they are caught of killed, they get replaced by a fresh recruit. (To match SE4, you'd have 12 leaders at any one time)

The intel points generated by your facilities could be used to train (and maintain) the agents and leaders.

You could hire basic agents pretty cheaply, but they would have a low success rate....
Agents could be upgraded to specialists (demolition, surveillance, infiltration experts, sleepers, etc) by spending more intel points on them.

You'd assign a set of agents to each leader, depending on the mission at hand and the skill of the leader.
The leader's skill could multiply the effectiveness of each agent.

Success would then depend on the effective skill rating VS the mission parameters, plus a bit of luck.

EG:
- The farther the target is and the more agents going on the mission, the more infiltration skillpoints required.
- Sabotage missions would require demolitions skillpoints, the more you have, the more damage you do if successful.
- Surveillance skillpoints would be required for defense projects (requirements multiplied by the area to be protected (planet, system, empire-wide, etc) as well as information stealing projects.
- Sleepers would provide a bonus to your success chance, but would be used up in the process, and have to be placed on a specific enemy planet. They would also have a small chance of being discovered by ongoing defense operations. Placing sleeper agents on your own planets (expecting invasion for example) would be free.