New Atlantis is definitely my favorite city. I love how many districts there are, and the Well puts it over the top. Really captures that Star Trek Next Generation vibe of sci-fi utopia, but adds layers of reality in the poor district.
Cydonia is by far the coolest idea, the coolest looking city on the outside with the huge mining areas and tubes. The interior is not bad, I just wish it was a bit bigger. And I wish you did more outside. If they fleshed it out a bit more, it would be 1st place.
Neon is awesome, and is easily my 3rd favorite city. The concept is amazing, a fishing ocean planet casino area. The vertical layers are awesome. You can climb all the way on the roof, or go 2 levels down with the fishing industry areas.
Akila in concept is great, and I think it has some of the best texture work and looks cool. It just needed a bit more to it, and the circular rings design does make it a little harder for me to naturally navigate. It's the only city I didn't fully memorize in my head. It just needs to be larger, with more to it than some shacks and mud. Even Gagarin and Hopetown look significantly more capable than Akila, and these people are supposed to rival the UC. The outside areas in Hopetown with the large hanger are cool as hell, and Gagarin is one of my favorites. I think it needed a very large industrial district, and maybe stick it like into a giant red rock mountain. They got close, but not all the way there. These are some of my favorite cities in any RPG ever.
Can't wait to see the Va'Ruun city.