In case you weren't aware, you actually aren't stuck on a single planet as life-seeded anymore. You can colonize 0% habitability planets now, but it really sucks because they use up extra consumer goods, and I think food and amenities. It does make early game really challenging though since you have to devote so much production to consumer goods unless you run with low living standards for the masses.
I got a few economic issues that is to be expected when you push ship production over capacity. Rare resources however, are impossible to manage. Every single building upgrade use it as upkeep and raffineries take one building slot for only one job, and strain mineral even further. Building slots are a rare and finite asset in the endgame that make compensating for problems impossible.
If you have much of an energy surplus, you're probably better off buying the rare resources on the market. Or at least some of them. It's pretty much impossible to synthesize enough of them to upgrade everything, and they're surprisingly cheap to buy. In my last game I had an automatic monthly buy order for 25 or so rare gases, plus a few motes and crystals.
The refugees are causing overpopulation and unemployment. Overpopulation is only a mild issue because I got a lot of luxury that negate effects. But unemployment is terrible with that crime event that pop all the damn time. It's not even the economic strain that get me. Just that stupid popup window that interrupt me all the damn time !
I'm trying to build a habitat to offload the problem but I'm activating purges and will kill the refugees if I have to. My empire's values be damned.
What living standards are you using? From what I can tell you don't get the annoying unemployment popup if you're using Utopian Abundance, which makes it a lot easier to ignore unemployment but requires you to be egalitarian and costs a lot of consumer goods.
If you're not using Utopian Abundance then you might want to consider turning off acceptance of refugees and turn on the planetary decision to stop growth. Depending on your ethics it may annoy some factions, but that's the only way I could manage it in my non-egalitarian empires.
Managing planet is also a pain in the neck. You have to babysit constantly, all the time. Even when they are full. Look away for a second, you come back to bunch of issues.
Yeah, agreed here. After trashing the Unbidden I tried to finish the War in Heaven in my current game because it
finally triggered properly at 2480 or so, but it dragged on for close to a hundred years because the FEs ran out of ships and I could no longer destroy anything to make their war exhaustion go up enough to force peace. I started conquering their planets to just outright destroy their empires, which eventually worked, but I had so many planets and pops I just completely gave up on managing them. Honestly, I gave up before then when I had about 25 planets in my own empire.
I did what I could to manage them, but it just became so tedious I did what I could to set up building slots but halfway ignored overcrowding and unemployment and then completely ignored it.
In the process, I was surprised to learn that overcrowding leads to much larger stability problems (up to -20 looks like?) than just stopping planetary growth (-5).
I also had to eventually give up on that game. The War in Haven glitched out at the end too, and never ended, so I couldn't declare victory. I got the announcement that the War in Heaven had ended, but the victory screen kept telling me that I couldn't declare victory during the War in Heaven. Man, I now understand why people say they've never seen this even work properly, even if this is the first time it's screwed up like this for me.