I think the game is modelling futuristic societies of technocratic welfare capitalist (UC) versus libertarian (FC), but trying not to load them as good or bad.
It is evident all is not well in UC. Firstly, citizenship is restricted, "Starship Troopers" style, in return for public service. That's a hard comparison to miss. New Atlantis looks shiny, but has urban slums full of graffiti indicating police brutality. (Listening to conversations in New Atlantis will reveal a mission where you have to investigate a power anomaly - this will send you to one of these blocks, which are otherwise very easy to miss, shut away.) One can also note that the UC is kind of ruthless: the dodgy xenowarfare research, aggression towards the FC. You'll also find that they have a rather nasty secret hiding in one of their basements... This does not necessarily gel well with the fact that when you meet their leadership, they seem quite reasonable and well-intentioned. Although I suppose you can make the argument that even a more benign leadership are stuck with the system they inherited.
Interestingly, you'll come across people who also have harsh words to say about the leadership of the FC: that they are basically a bunch of self-interested twerps enriching themselves at the cost of their people: and indeed, some of them don't exactly seem very ethical. Elias Cartwright is a sort of "old money" snob, who wants traditional families to continue dominating Akila. Bayu appears to be little more than the top mob boss in an utterly corrupt city. Ron Hope... I haven't come across that much of him, but he seemed more interested in his company making money than anything else.
I think the game is telling us that it sucks to be poor no matter where you are. The UC poor are oppressed and denied even the vote. The FC poor vary depending on the local governance: the Akila poor live in shacks in the mud, begging the rich for hand-outs. The Neon poor are all exploited and victimised by what is essentially a corrupt state where the ruler is just the criminal with the biggest gang. Not sure I've been to a city in their other major system, but I'm sure it's just as shit.