good ideas, let me add:

classical sabotage: has a chance to kill enemy ships or structures. should come at a price, eg. resource price, drop of relations, temp. loss of immunity, whatever.

rebellion: changes planet ownership. only works when allegiance is below 10 or even 5 or at zero. it means you can weaken it with culture/ envoys and then have them take the whole thing over.

sabotage defenses: lowers planet health ie. infrastructure.

also, I thought about using envoys as counter intelligence also. sort of like researching the option and the get the ability to expel  enemy envoys (only works in own territory, units are not killed, but forced out/automatically jumped back), perhaps also at a price as above. alternatively, they could locally give you the ability to lift immunity.

We have a couple of neat ideas in mind for additional abilities along these lines. Stay tuned over the next few weeks for more info.

Id also like to add that we need some race specific diplomacy and espionage options. As of now they are all the same. Im assuming this will change

What if the TEC Envoy ship had a expanded version of armitice that stopped all hostility if one of your wells comes under attack? I mean that what diplomats do they stop conflicts. The cool down time would be enormous something like fifteen minutes. Also the unit cost would be huge so each faction could have no more than two per team.

indeed, diplomatic envoys and sabotage crews are just not the same. hm, I would have an idea for this also. maybe there could be two separate ships, one for the peaceful things like embassies in this case and one for the nastier stuff. that second one will have to be either cloaked or disguised of course. hw: cataclysms mimic was a nice idea in that respect, though it might be a bit hard to fool a good player with it. still, though, appearing in the disguise of your enemy's ally as some trade ships or scouts sounds like fun.

another idea maybe for peaceful ai use: an exchange programm that enables members of the species to work and live in the other's territory. gives boost to culture rate ( gameplaywise I'd prefer max. allegiance, but you can hardly justify than with any logic) or research or sth. needs to be refreshed every 20 minutes.

embargo (thought that sort of overlaps with the sova's ability): it could slower military research. think of today's UN embargo vs. Iran which does not exactly make it easier for them to research their stuff. or it could lower construction rates, incraese cost, ... but again, pretty similar to sova stuff.