Having a few more SM options would be nice. For instance:
1. Having a geo-survey and grav-survey ship store their survey information inside their computers as 'intelligence inside ship's computers". The ship would then have to either take it back to base, 'transmit' the message through a jump point, or hand it off to a currier ship. This information can therefor be lost if the ship is destroyed before the intelligence is gathered. This 'intelligence storage' could be used by reconnaissance ships as well, requiring ships to scout out enemy ships to determine intelligence information, such as speed and armour level. Optional: have a limit to the amount of information that can be stored, in billions of bytes, the ability to add 'custom' information (read SM) into a ship, adjust the size of information, 'corrupt' or 'vague' information to make it less useful to the players, and encrypt information to make it harder to crack.
2. When 'transmitting' information (such as intelligence, orders, personal communications, fleet updates, etc), allow players, espionage teams, EW ships and god(SM) to jam, intercept, decode, scramble, manipulate, trace or retransmit the signal. An SM 'transmit' button can be used to run the function, which would check for the nearest ship or base in range during the next sub-pulse, and place the intelligence in that ship/base. A signal detailing geological information of another solar system can be transmitted through a jump ship, which could then be picked up by a nearby intelligence cruiser. The data could be encrypted or compressed, requiring the ship to try to decode the message. By the time the ship does so, it may be too late to act on the information.
3. Allow the SM to set up espionage scenarios, with generic types such as espionage, sabotage, theft, surveillance, assassination, counter-intelligence and reconnaissance. Allow the player to name the operation. Allow the computer or SM to determine the difficulty, cost and reward for the operation, through die rolls and DC ratings (or the enemies die roll). Alternatively, the computer could just use the espionage team's skill rating for it's die roll, and the enemies counter-intelligence skill level for their die roll, +/- funding situation. The SM can then reward the players with whatever the player was targeting, such as ship schematics and so forth. The chance of it being clandestine or covert is dependent on the type of mission and the SM.
4. A communications system, as Zook said, that is used to transmit large amounts of 'signal' to other ships. Maybe have an optimum range and an absolute maximum range. Ex: Radio Antennae; 100% effective up to 1 billion km, dropping 1% in effectiveness every 100 Mkm after that. Sending a message to a ship at 50% effective range reduces the power of the message(so it might not be heard), the clarity(might not be understood), or it might distort the signal(might not be recognizable). The SM should be able to create these components as he sees fit, maybe even requiring them to be researched by the players.
5. Allow officers to be traitors for other players, by giving the players the ability to blackmail, kidnap, extort or coerce. These officers could then be sleeper agents, or actively working with the other side. Examples include helping the espionage team steal important documents, have the mole obscure or block investigation, or actively participate.
6. Moving away from intelligence, cities. Maybe have a little box in the planet window saying how many cities, towns and outposts there are on a planet. Nothing major, just for fun. Maybe make it so that the enemy can capture a city during ground combat, so you can see just how many cities you have left. Maybe a separate box showing the number of metropolises, and the top 5 by name (if there are any on that planet).
7. Scandals with officers and administrators, related to their personality. Make it so an aggressive, assertive, ass****, (I'm sure that's a personality) may get into fights with other officers. Again, nothing major, just for fun unless the SM says otherwise.
8. Adding and removing unrest to a planet in SM mode. Mobs and riots, maybe even insurgents.
9. A insurrection command that determines if a ship, fleet or planetary garrison separates from your empire. Maybe input a percentage or base it off unrest. When the function is called, search through all ships relevant to the conditions set (such as it's faction and location) and spit out either rebel, loyalist or split. The split ships can then determine it through boarding (except their boarding their own ship).