So, I was thinking it would be cool to be able to make a special ops detachment unit, in line with the new citizen system and invasion mechanics. It would occupy an area between the spy and the legion, without replacing or overwriting either. I have a pretty solid idea of what missions it could have and the form it would take, but it's not a perfect idea yet.
In my mind, the spec ops unit would be a mission built from a shipyard, with 4 missions split 2 on offense and 2 on defense. It would be a one shot unit, utilizing the movement style of the treasure hunter. Upon build completion you would get a mini-screen in the style of the trading ship or transport/colony ship launch to choose a destination. Once the unit arrives (if it isn't destroyed in transit, similar to VIP transports being unarmed high priority targets) you would get to pick a mission based on whether you are using the unit for a defensive mission on one of your own planets or offensively on another faction's planet. The 4 missions would be target building (offense), target citizen (offense), target spy (defense), and resistance training (defense). The abilities themselves are rather powerful, but balance would be achieved with several limiting factors. Their build cost would be individually moderate, so mass production would be difficult, if not impossible (perhaps using a bunch of the Thulium that sits around mid-late game). The tech to unlock them would be somewhat deep along the spy or invasion tech line, allowing spies to be more effective in the early game. And they would have a moderately high chance of mission failure (somewhere around 30-40% maybe?) due to their high-risk high-reward nature. In terms of the offensive options, there would be 4 possible outcomes: mission success (non-attributable), mission success (forensics or method analysis allow them to identify the perpetrators), mission failure (non-attributable), and mission failure (team gets caught). What this provides is another option in a range of behaviors, as targeting an important building for destruction rather than disabling it (or assassinating an important citizen) would be a serious provocation if it was discovered by a faction that you are not currently at war with. The defensive missions would simply be success or failure (I can imagine some humorous text maligning the population for a failure to learn more effective resistance techniques).
It has always bugged me that the only way to counter a spy on your planet is by sacrificing one of your own spies to kill it. When a spy moves to disable one of your buildings, he is performing the role of a saboteur, which is a more overt action and I think most would take a more overt response with a team of hunters to get rid of said saboteur. Target Spy would allow a player (or computer) to remove a saboteur from their planet without having to lose one of their own spies. This would allow those who have a spy deficit to counter individuals who mass produce spies to hold down tech progression or manufacturing aggressively.
So how would this fit in with invasions? Not so much directly, as cool as it would be to have a mini-legion I can't really think of a way to incorporate them easily. But prior to an invasion you could send one ahead to take out the general on the planet. There could be more missions too, the 4 I listed are just the ones I came up with today.