I think, that what Tewelvefields is saying is the same, as what I'm saying. The scout ship in the game, is there to gather data, and a spy ship would do the same as well as some spy like functions. That why I said, it sdould be more of an upgrade.
Here are my ideals, for spy missions for the TEC( I have yet to come up with any for the other factions).
1. Build pirate king: This is were your spy ship goes to a pirate base, and if the pirate attack, is against any one other the you, then you can use this abilitie. What this abilitie does, is turn your spy ship, into a pirate version of an level 1 capital ship for the TEC faction. The pirate king, can not gain exp, so will be at level one, no matter how many ship that it destroy. The pirate king, also lets you control which planet gets attacked, by the pirate group, but only the planets, of the faction that has the highest bounty can be selected. The reason, for this upgrade, is that the pirate faction when it attacks is very easy to stop, with the right planetary defense system. Also the TEC can win most of the pirate bounty wars.
2. Q-ship: which is an upgrade to TEC's Insurgency. Which allows you to have more conrtol on when the insurgency happends, as well as the ships in the fleet. What I have seen is that Insurgencey, hit the same worlds, that the pirate attacks normally do. This means that there is all ways a defense system to counter a pirate raid. Pirate raid fleets, normally have a lot of ship, form 15-50 I think. While a insurgency strike force has only 6! Which means that they are all ready countered, by the same system that counters the pirates.