I think each city should at minimum have either free support for 2 troops or +2 to +3 gold income for the purpose of wages.   The basic militias don't keep the really nasties out and you have to defend your cities.   

Also, I think the first two heroes (or even three?  Maybe all since the hero mechanic has been improved)  should not cost wages.  Bocco the idiot comes out as often as the plague and its just a hammer to the early game econ.   But hey who turns down a free unit?  A hero at that.  

The early game is supposed to be slow, granted.  But is this slow or choked off and stifled ?

Never have problems once I have a couple of towns built. I literally am flowing in gold by mid-game. I never even have to raise taxes above low in ANY game.

specialize your cities to avoid that kind of problem. use tiles with essences for conclaves, high production tiles for fortresses and build towns on those mediocre 5/3/0, 3/4/0 or 4/3/0 tiles (depends on play style - spam lots of simple units with high production fortesses or use those production heavy tiles for extra towns and build only one or very few high essence fortresses with damage/inititiave/defense enchants and rush buy elite troops with all that excess money from the towns) 

towns are there for cash and faction food - they don't really need the extra unrest reduction from the essence based buildings (cleric/shrine/temple) since both their production and their research aren't very important. if you have the choice, pick locations on rivers since the pier/harbor buildings increase both, gildar and growth, which are the main strengths of a town.

a few conclaves on high essence tiles can produce crazy research (especially in the mid/late game once you add an alchemist and the research percentage buildings). concentrate your research there.

focus the towns on gold (merchant, market, well/inn/festival; if it's on a river  also pier/harbor/water mill line). keep in mind that food translates into growth, so don't neglect the +food and faction food buildings either. a base town (level 2) has 4 gildar base yield, a level 3 town has 8 base, a size 4 town has 12 - so growing them to higher levels also gives you more cash to filed larger armies. skip the research buildings in towns until all available money and food buildings are built - a bit more research is nice, but a single decent conclave produces more research than 3 towns combined, so don't try to get everything everywhere. specialization is more efficient than trying to balance all settlements to produce a bit of everything.

you may also want to use one of those 1/5/0 forest tiles for a town. it will take a long time to even reach level 2 (you'll need some agrarian tech, a granary and probably some faction food buildings) but you can use this site to get the treasury vault and brewery built fairly fast once you unlock those buildings.  

No your computer just doesn't like you... just like mine doesn't like me.