In general, I agree with your observations...but I think more than just the supply pact needs to be nerfed...I think the Vasari envoy bonus Mutual Threat is ridiculously overpowered...I've played 2v2 games against a team with a Vasari ally and that envoy bonus alone made it extremely difficult...
Let's look at some numbers here for envoy bonuses....
Arbitrate tariff gives +50% trade for 60s out of 180...or about 16.7% constant trade bonus...pretty powerful...and probably fine...
Cultural Assistance gives +50% culture for the same time period...so on average 16.7%...problem with this is, since it ain't constant it really doesn't do a whole lot of good... even if 50% is enough to start overthrowing a world, the 2 minute break between cooldown and duration pretty much guarantees you'll never make any headway...culture is too slow, this ability doesn't do squat....I'd recommend reducing the cooldown to 60s and reducing the bonus to 25% (or somewhere around there)...if the ability is constant, the culture bonus will actually be meaningful...problem with culture bonuses is that it's all or nothing...if you have enough culture to hold your own, any more is worthless unless it helps overthrow another planet...
Grant Amnesty makes the planet immune to bombardment for 25s...cooldown is 180s, so I'd say this ability is fine...sure, it can be really powerful and help resist even a novalith, but the short duration and long cooldown means it requires good timing and can still be easily overcome...I think this ability is fine...
Mutual Threat...this ability is ridiculously overpowered...brings ship construction and structure construction times to 1/3 of their original values AND it triples resource income!?!? You got to be kidding me...even if its only 60s out of 180s, that is still overpowered...this ability needs to be on par with arbitrate tariff...a 50% increase in resources is not quite as good as the trade bonus from arbitrate tariff, but this ability also allows you to build ships ridiculously fast...I say change the resource boost form 200% to 50%...I could even see 75%, maybe even 100%, but not 200%...
Nanomedicine outreach restores 250 planet health over 10s and has a cooldown of 180s...that isn't very good...I wouldn't bother to argue making this ability more powerful since Vasari have mutual threat and Grant amnesty, but under the assumption mutual threat becomes a reasonable bonus I think the cooldown on this ability needs some help...250 health over 180s? I say make the cooldown at least 60s so this ability can be useful...
Quell Unrest...adds 5% planet allegiance every 180s...now, since culture is slow, that is somewhat understandable...but if the Vasari envoy can allow a planet to completely resist a novalith, I think this ability should then be capable of resisting a deliverance engine or at least mitigating its effects...an increase of duration from 10s to 30s would be a start...that's a 15% increase...
Sacrifice...relationship increase needs to be more than .6...it takes a long while to get envoys in the right place sometimes, so if you're going to have to replace one, it better be worth your while...not sure what number to put here but definitely more than .6....
Settlers is fine...its not great, but it's okay...TEC make up for it elsewhere...
Worthy cause can give the player 60 credits every 30s...that is 2 per second...I think that is pretty good...no need to improve this...
I have opinions on the pacts, but I'd like to keep the focus narrow so we can get specific changes and then move on...
By the way, good call Zombie for getting this thread started...