First off, this is really heading in the right direction. Loving the changes overall.
The things I feel need to be looked at are:
1. Allow an option to flag cities that finish their production and have nothing left in the queue - including cities that finish production of a resource.
2. The green and yellow 'Turn' button is too similar for colour-blind gamers.
3. Levelling of heroes would be great if there was a bit of randomisation in the pre-set choices. What I mean is you still have a set of choices for each hero but that the game shuffles and adds or subtracts some skills the first time they gain a level. Also, the current choices are a bit 'boring' overall.
4. When upgrading armour or weaponry it would be great to be able to pick and choose exactly what you are getting during the upgrade. For example, a unit specially designed to defend and counter-attack becomes less valuable if the sword is later replaced with a mace or axe.
5. Combined arms doesn't really work in the tactical battles because of the random starting placement and lack of real combat difference between cavalry and infantry (and the weapons used). There is a real opportunity here to use a rock-paper-scissors bonus system to make the army design choices more meaningful and to reward combined arms. Why would anyone not design an army of cavalrymen the way the game currently is?
6. Would be good to be able to upgrade the unit size as that tech becomes available.
7. Need to be able to easily highlight any resources that haven't been developed. Perhaps some sort of cloth map filter or highlight.
8. In tactical battles it would be good to be able to turn on coloured bases to immediately identify which troops belong to who.
9. Archers are slightly under-powered. You can sit back and drink up a lot of archer damage but can't do the same for infantry. If they were a little stronger (attack or initiative) then it would become more important to reach them (which could provide a good use for having cavalry in armies if infantry gave you higher attacks and defence but that cavalry gave you higher dodge vs archery - rock-paper-scissors).
10. Please keep splitting the XP by the number of heroes in an army but I'd suggest you explain how the XP is calculated in the battle results screen so that new players are informed of what is going on. As it currently stands you must know about this mechanic in advance so there should be some sort of feedback about this to the player.