Yea I'm really not liking the sector system. In addition to everything you said, the late game is really dry because you can't manage your planets, you just sit there watching resources accrue.
There is a mod to up the planet cap to 999, I might try that.
I don't know that adding the micromanagement hell of direclty controlling another 50 planets is what's needed here.
The game should do a better job at becoming more grand strategy at that point. Planet management should take a back seat to larger issues.
Basically that mid game needs to be beefed up with better diplomacy, more aggressive AI, more in depth internal politics issues that ar enot as easy to sidestep, and a more in depth economical model.
Basically it should go:
1. Exploration/colonization/planet management. The game already doe this well. It then should slowly cede to:
2. Early diplomacy. Skirmishes, early alliances, simple trade deals, building up infrastructure and early, simple, internal plitics. The game pretty much stays here instead of moving to
3. More complex diplomacy. Large scale wars that demand more complex logistics. Internal politics that require attention and decision making and compromise to handle. The ability to help build up and stabilize allies, and destabilize posisble enemies - via espionage/manipulating markets/other diplomatic channels.
You should be in the mid to late game and asking for more plantery micromanagement. There should be plenty of larger scope game mechanics to kepe you busy. And those just aren't in the game yet.
I'm sure they will be, as the beef up that mid and late game, but we'll have to wait.