I don't know the answer to this but I'll just write a little about what I am currently experiencing while designing Stardust and playing other games.
I play a lot of games with my wife, both tabletop games and video games.
We both enjoy a wide variety of genres and among them are strategy games: we played a lot of Starcraft 2, a lot of Risk, and others.
In games that are specifically designed for two players, you obviously don't have this issue... because they set out to be 2 player games, however with competitive games that are designed for more people, it feels like there always needs to be a way to mimic a 3rd player.
There's nothing wrong with that at all. I much prefer that to "each player controls two characters/armies".
Sometimes this 3rd player is made in a way that they don't even feel like a 3rd player.
Take Risk for example, in the 2 player rules there is a neutral army that just sits there and defends itself. When a player gets reinforcements, the neutral army gets half as much.
This way the third army acts as a nuisance or as a buffer between the two human players.
I enjoy the idea of a neutral army but I don't think anything about it should be decided by the players.
The reason being that if I have power over this 3rd player, I'll use it to make life hard for the other human player. This can mean that it further propels me to victory or completely turns the game around and makes me lose.
Lets take Risk again, I cannot attack using the Neutral Army but I can place reinforcements depending on how many I get.
So if I'm in the lead I'll also be in the lead at placing reinforcements for the Neutral Army, which means I can slow the other player down even further.
We did a few experiments to try and solve this on Risk: At first we just tried to reverse the situation, i.e., the player who's not playing is the one that places down the reinforcements. This just made the game last for a long time.
Then we tried to make it a fixed amount: just 3. This actually worked well in the beginning but we quickly decided to scale it up to always the average of reinforcements between the two players. It worked better but it didn't feel great.
Then we started thinking "Well, we've got no idea what we're doing and way smarter people than us did these rules", so we gave up for a bit.
A few games later we decided to try out the average mechanic too but also include a special rule that said if a country owned by the neutral player had over had 1/3 more troops than a nearby country, then it automatically attacks it.
This brought a lot of tension to our games and now the 3rd player had an actual presence.
I'm not claiming this is the best rule ever, but this is how we like to play.
So back to Stardust!
My wife is my number one playtester. Stardust was made for more than two players but we still play it a lot, just the two of us.
When there's many players, they keep each other in check, but with just the two of us, we don't do anything but attack each other and if we don't, we risk the other becoming too strong.
This is particularly true when playing against the Hivemind who is, by design, quite aggressive and achieves a full fleet faster if left undisturbed.
I've been toying with the idea of making the Hivemind an automated 3rd player for the 2-player variant but I don't want it to feel forced. I've not figured it out completely yet. (Ideas welcome!)
Thematically, the Hivemind is native to this system, so one of my ideas is when a planet is flipped there is a Hive there with full population. Every time a player turn starts, two pops are converted into drones on any revealed hive.
This will work much like the neutral player in Risk, but I think would feel a bit more natural, but I still need to test and improve this.
Rahdo talks a bit about this in his interview with Gabe on Board Game Design Lab, and I plan on verifying this against the points he mentions.
As always, ideas are welcome!