There were some unintuitive moments during my first game and I thought I'd give feedback now, because otherwise I'll get used to it or find work-arounds and don't notice these "issues" later on. But new players might be having the same difficulties as me, so here it comes:
1. Happiness-Wealth-System - micromanagement hassle: Don't like the constant (nearly every turn for all colonies) adjusting of the sliders on a per-planet basis to keep happiness at 100% or 50%, but not too much above it. Tiring and no fun. Too complicated (why jumps in bonuses and no gradual decline? - urges me to micromanage), better get rid of it or simplify it: I want to understand what is happening and why and keep happiness at a predetermined level (planetary governor), if it has to stay in the game.
System in Master of Orion 2 is still my favorite in that regard.
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these other things are minor in comparison, but I noticed
2. Cataract (Tile property) says it gives +1 level to research, but doesn't
3. Typo at "High Approval Bonuses": "Influance Growth" instead of Influence with e
4. Sent constructor to starbase to upgrade it, didn't immediately found where to do it (upper right corner) - maybe a prompt or stronger highlighting?
Also sent Constructors to Starbases but wasn't told they had arrived - squandered a few turns and send more Constructors there then I needed ...
5. Is there a way to launch constructors from Starbases again, if I don't want to upgrade any more (I sent 4 ships there but only needed 2 upgrades, but couldn't send the constructors elsewhere, once they were on the same tile as the Starbase)
6. Happiness buildings not working as described (and couldn't even build the higher-tier approval buildings, even though I researched them) - combining all the bonuses and subtracting all the negatives I had like +80 % happiness and should therefore have been at 100 % (180% theoretically), but was way down at 30% or so ... why?
7. In managing the total production output, it would be nice to have a sum of all the listed bonuses (when you have like 6 different sources for bonuses, it get's tiresome to add them all up by oneself) displayed, as well as the base-value (derived from population, I think).
But as I said, adjusting all the sliders for all of the colonies all of the time (being incentivized by the discontinuous bonus-malus-system) is so tiring and broke the gaming experience for me 
I had really hoped Galactic Civilization 3 would make the game mechanics more transparent and would require less tiresome "work" to keep the colonies at an optimum performance, so I could enjoy the game and strategy instead (had the same problem in Galciv2, but not in Master of Orion 2 or Civilization V, for instance).
I would recommend, they take out the happiness-mechanic or make it independent of the production wheel or at least make the bonuses continuous, so I don't have to fumble around with tiny adjustments on the production wheel every other turn for each colony.