Iv'e been thinking about this. Ideally, you want some way to force the player into conflict, but have that conflict provide opportunity at the same time. As it stands, the way the core game does this is mainly with commissions. Taking a commission from a faction effects your relations with all other factions, thus forcing the player into conflict with their factions enemies. This falls short though, because instead of providing opportunities it mostly just provides capital, and that quickly spirals to ungodly amounts of money.
I think a good way to balance the mid-game would be to change the way commissions work. Instead of just providing fat stacks every month for taking relations hits with the other factions, it should provide unique missions that offer higher rewards than other missions. This makes a little more sense too. If you work for someone, they are going to want you to do things for them. These missions could be things like "acquire specific rare salvage" to "eliminate specific target fleet in other faction" (the same way bounties spawn). You could have missions to smuggle types of illegal cargo out of an enemy port, missions to protect a trade convoy, basically anything you can think up.
Additionally, change the spawn frequencies for some types of rare salvage and provide alternative ways to acquire them to prevent the explosive power spikes the game gives you. I've pulled half a dozen synch cores in my last game over a few expeditions, and thats an insane amount of money for the size of my fleet at the time. Reduce that, and balance it by putting them in restricted military markets for sale (so you can still acquire them for your colonies when you need them) that requires max rep and a lot of capital.
Add more types of missions in general! Right now, we have, examine ship/probe, survey planet, and bounties (plus deliveries from the bars). Basically 4 types of missions. Thats almost nothing! The sky is the limit! add whatever you can think up.
(Also, let me hand in planet surveys the way you turn in AI cores. I just think that would be neat.)
