I try to give them names which help me remember what path I want them to take. I'm not so plain as to call them ' Conclave 01, 02, 03' but I will use things like 'Riverside Village' to denote a future town, or 'Druidic Circle' for a conclave.

A long standing issue. I name my cities "FireIron 432", etc where 432 is the food/materials/essence. This is (for me) the key factor in what a city will be designated (3+ essence = conclave, first 4+ materials, and chokepoints = fort, all else = town) and lets me see city (potential) quality at a glance on the world map. I have also experimented with tagging a letter at the end "Riverside T", "Tarthchoke F", "Crystalgrain C" etc.

Even if there was simply a button which toggled between the decision and the city details screen (with no way to exit these two screens until a choice was made), it would be better than the blind pick system for people who don't use a naming convention.

Agreed.  There should be some function to allow players to make 'informed' decisions.

I also like naming my cities to give me level-up hints.

However, note also that you can use your arrow keys to see the city itself and the surrounding tiles.  This is not ideal but it's better than nothing (except, of course, when you are renaming the city and are using the arrow keys to position the cursor within the name).

The popup dialogs really break the flow of the game all to pieces.  Stardock should consolidate all their messages (including level ups and carravan destruction) into the quite functional asynchronous notification system the game already has (the messages on the right-hand side of the screen).

In this case, when a city or champion levels, the player gets a notification.  Clicking on that notification will center on the champ/city and pull up the champ/city details page.  On the details page will be a shiny button that says "Level Up".  Clicking on that will bring up the choices for leveling.  And if you still aren't sure, you can click "Nevermind" on that dialog and simply come back at your leisure to pick your upgrade.

Exactly what Rhaegor said. The information the city summary provides on level up is not the RIGHT information, for me.

For my play style, the decision about what type of designation a city will get is based upon a city's eventual potential yields, not its current yields with buildings and enchantments. This is even MORE true without any reference to what buildings and enchantments are in effect on that particular city at that particular moment in time.

In the level up screen: Grain can be seen hovering over Food. Materials can be seen hovering over Production. And Essence count is between the too (iirc). Try hovering over thing things if interested, should be similar to the side bar on the city screen.

I don't tend to have a problem with city management. So no real comment on the topic.