I had some Ideas regarding diplomatic options with prewarp Minors:
Unlike other Minors, the AI of primitive (prewarp) Minors shouldn't be able to initiate contact on their own (be it for warnings, treaty suggestions etc).
An additional diplomatic Option 'establish protectorate' or 'guarantee independence' could be added to allow Players to deter other empires from conquering (primitive) Minors without an official alliance (e.g. for those who want to play with the Prime Directive in mind, or if relations with a Minor are too bad for an alliance but you want to keep your rivals from expanding in that system) - it could trigger an alliance if the guaranteed Minor is attacked or (if a system similar to Paradox's 'casus belli' system will be included in the game) allow the player to attack the rival who violated his guarantee later on without a drop in morale. If a (primitive) minor joins an empire peacefully, the guarantee would of course not apply.

On a completely different note: What do you Guys think of establishing a subforum here for After Action Reports once Supremacy is officially finished?

That sounds like a good plan all on points.

I'm happy to hear that.
Here is another suggestion: If during a war with another empire you conquer a system inhabited by a minor race and previously subjugated by your enemy, you could enact a decision (perhaps via the diplomacy options with said minor race) to liberate that system, releasing the minor and giving you good relations and a military alliance with it.
So for example if during the Federation-Cardassian border wars Starfleet managed to take control of the Bajoran system, they could release Bajor as an independent world with an alliance with the federation.

Another minor addition that would allow for more strategic depth would be giving minor races territorial claims on the space around their homeworld analogous to those of empire colonies once they reach a population threshold.
This way getting a minor race to join your empire would not only add a densely populated system to your empire but also 'free up' potential colony sites close to the minors homeworld that were previously off-limits due to a non-aggression treaty and the mutual recognition of territorial claims such treaties entail.
If the player decides to colonise a system within the claimed space of a minor that should lead to a distinct drop in relations and depending on the minor maybe a declaration of war.
It would also add more importance to affiliation treaties - you would not only get a refuelling station for your ships but also possibly get the option to expand in a direction that was previously blocked by the territory of other empires and hostile/neutral minors which left no unclaimed space to travel through.