Are there any non common city buildings for city levels?

no. There used to be uncommen and rare city level improvements as well as traits for champions, but it was dropped and changed to the current model of fixed improvements and traits to provide the player with a projectable progression.

While it could be a lot of fun to get suprised by the things you unlocked and it definitely increased the randomness of the game a lot, it was also very frustrating if you got all the things you didn't need while you were already a big chunk into the game.

There was a mod for an earlier version (not sure if it was LH or FE) that offered rare level ups that happens every four or five cities - including a "Prophet" improvement that added 2 essence for a Conclave city.  I kinda liked how they were much better, but you only got to choose one every four or five city level ups.  Someone could perhaps go for a look on the forums to see what the changes were.

This would be AWESOME!

Not having your city levelups pre-planned and always so...linear....would be a fantastic way of mixing up the game and adding in that rpg spice. I would LOVE not knowing what my 3 level up options are going to be.

Yeah I'd love some random rare levels restored

The main issue is probably that you need to make room for the  new random improvements (ElementalDef only allows 3 at a time) or make it possible to "lose" the regular ones with RNG as well. Don't think it's too hard to do, and you can always steal some code from my last Conclave army mod, I had some "great fun" finding out how to create a new Tower of the Magi there for the level 5 conclave level up.

You can define how many different choices you have for the city level up perks in Elemental Defs file.  If you make it 100 and there are only 3 choices it will show only 3 but if there are more it will show up to the new max.