Well, even the regular game civics aren't perfectly balanced either. Police State might as well be blank, Vassalage is kind of niche unless you did some kind of Feudalism sling or just going to a quick conquest win, and Free Religion is driven far more by diplomatic needs than by its own effects. So a few misses in FF are acceptable.
Mojo, your expression for growth of one population per 7+(30/popsize) turns of Utopia rings true. So the typical rough numbers might be 10 turns of Utopia to grow one extra population at sizes around 10. Roughly, if Utopia increases your pop by 20%, it breaks even against its own penalties, assuming Green and figuring opportunity cost of Mechanized. So it reaches breakeven production after say 2 growths, then after 2 more growths it will have made up for the time it spent penalizing you.
So even barring anarchy, it takes in the neighborhood of 40 turns to show any profit. Longer considering the new pop goes on bad planets. Longer yet considering food lost to exceeding the health cap. Longer yet considering systems that get nothing from Utopia since they're already maxed on space or happy, which for us was a third or so of them. And the anarchy makes it completely prohibitive before hitting the end of the tech tree.
And that's figuring the commerce as a simple penalty. That's not quite true, especially stacked with Green's penalty. Remember it penalizes all commerce, not just the surplus going to research. If you have 100 commerce of which 60 pays expenses, then -35% commerce knocks your beaker rate down by 87.5%. So I'm afraid Utopia just isn't paradise.
Pacifism is insidious. It looks really strong, but you can't switch to it when you first get it - the exploring scouts and PDSes cost too much money as we discovered here. And it produces nothing until a system has 7 base hammers, which takes until size 3 or 4. It's definitely a profit once several systems are up to size, and pays back simple hammers for the anarchy within 7 turns, but not too early.
Technocracy is disappointing, living in the shadow of mighty Monarchy in the same column. I think I do understand why Monarchy is in the game so early, though; it checks ICS by providing a viable alternative of growing the capital. Without Monarchy, a new pop point in a new system with the free facilities would always be more productive than a new pop point in the capital. Monarchy should at least have had higher upkeep though.
Planned may as well not exist, coming so late on the tree and off the ascendance victory path.
I would like to see stronger civics in general. So many of them have serious drawbacks that it's debatable whether they're a profit at all. And the anarchy cost makes them a clear miss. Almost no civics in the standard game have a drawback, other than upkeep cost.
Late game growth - I suspect that it is correct to build a 2nd nutrient facility in most systems to speed growth up to size 10 or so; if this is done it is unlikely that growth can really be leveled off afterwards although it will be slow.
I use one Hab Facility per system as kind of a proxy for nutrient facilities. If there is an Earthlike planet, a hab facility is strictly superior to a nut facility on a size 2 planet (+2 food by upgrading a laborer from 2 food to 4, and you get it sooner with 1 laborer instead of waiting for 2 to fill the new planet), and usually superior to a size 3 nut considering the new pop works the free mining facility as well. Definitely superior to a 3rd nut.
Later hab facilities are almost never worth it. The best case for hammers is putting an otherwise unworkable pop onto a 1-4-4 improved gray planet. At 160 hammers for the hab, that's 40 turns payback, and only if you had a gray that was worth a mining facility. Extra habs do have some use in transforming hammers into commerce by putting population on a gems or blue planet.
The payback time for a nut facility can be worked out similar to Utopia. The most typical case is the 2nd nut facility at 100 hammers on a size-3 world for +3 food. This creates an extra population after 22 turns at size 5. If the extra pop produces 3 hammers each (reasonable considering a mix of orange/gray/gems planets and hammer civics), it pays back for the nut facility in another 33 turns. Less than that considering it helps produce intermediate pop sooner, a 2nd or more pop eventually, and commerce along the way. So I agree with that instinct to build a 2nd nut facility in most systems.