There are some factors to take into account, depending on your play style, as said above.
I think that most important city will be your fortress, as the place where you train your better units. The fortress will be better as you get more warfare techs, so it will take a long time to fully develope it. And you will need some towns, to provide the faction food necessary for it to grow. So having more than 1 fortress is contraproductive: for each fortress, you will need at least 3 or 4 towns. And other 3 or 4 for each conclave, for the same food issues.
If you agree with those points, then you will have to wait for, at least, a X/4/2 tile to be a fortress. It is preferably it will have access to forest, as a logging camp will give you 1+ material. Clay pits are highly recommended for the same reason. The 2 essence minimun: first for hammers (to build faster) and later for 2 auras for your units.
Cities with essence, but not too much production, can become conclaves. They will benefit with research spells (inspiration, etc). But remember that it will take long to have a good output of reserch (techs + buildings like sage etc.).
All the rest will be towns. Towns must focus in groceries, bakeries and butcheries. These will provide the faction food needed for growing the rest of your cities.
So, if you already have a good fortress and an acceptable conclave or two, I prefer having 2 towns providing food than a more centered bigger city.
If you don't have them, then it is better only a big city that will become the fortress or a conclave (assuming that you will be able to settle enough towns in other places).
And remember: the best fortress will only be one: many essence and production, and the "warfare 1 per faction buildings". Explore as much as you can, because if you develope a fortress and then find a better place for a fortress, you'll find that having two fortress leads to not enough developing due to food lack (you will need to settle more towns).
Anyway, if you have many towns, you can have a second fortress for training cheap units or while building improvements in the main fortress. I had a second fortress for that reason, but in my last games, I'm trying in dealing with only one fortress, and focus in more conclaves and towns. After all, remember that once war starts, you will get some AI cities wich usually are well developed fortress.