...Am I missing something obvious?
More like a bunch of not-so-obvious things, especially if you're still thinking a lot about MoO2, which I loved also. The class 0 worlds are indeed unusable, for example. I don't know which version was on sale, but the first expansion, Dark Avatar, did add extreme environment worlds, but you can still see plenty of PQ 0 worlds if you keep habitable planets low in your map settings.
Re people being 'unhappy,' there's a wide range of what 'too unhappy' might mean, but basically you don't want to build a farm on your homeworld ever because it has a much higher starting pop limit than your other colonies. You get a double-growth bonus when you keep a world at 100% approval, but you don't start losing pop until you drop into the low 40s (below 41%, I think). Basically, if you're a hardass, the game lets you whip most of your people without risking serious unrest.
Re starting in the corner, that really depends on your map settings and what sort of corner they generated. I only learned the word recently, but apparently I'm a turtler, so I really like a good corner to start my games. For me, 'good corner' means that it I can get most or all of the high PQ worlds in the area before any other player shows up. But I like gigantic and immense maps, and I'm pretty sure that corner starts grow harder as maps grow smaller.
There's a GalCiv wiki that might help you more than the manual, and the forums still have several experienced regulars who try to answer 'rerun' questions. You can also add site:forums.galciv2.com to the end of your search terms at any good engine and get results limited to this forum. For example, you could enter
population morale site:forums.galciv2.com
And get about 149 hits.