I would like to throw stuff in here too.
Agree with the city/wall layout, if there was some kind of limit to cap the walls, if that's really not possible I'd be happy with pre-decided walls but open plan for buildings inside. Just for the feeling of having a unique settlement.
Reduction in some of the building times.
this may just be me, but on one of the elf quests I was defending with an npc elf army and they were purple, I was blue. I found it difficult to distinguish my men from theirs. So perhaps just a tweak on the boldness of colours?
Not requiring your hero being present to complete the quests. Maybe just when he arrives back to home town you can complete and get your rewards.
Rather than highlighting your troops, making them go white - which I feel spoils the look, having small bold circles at their feet.
I quite like the idea of using resources to make other things, for instance using wood to make planks, to make boats etc. it may mean speeding up gathering but it would also be a way for people to use excess rather than just selling etc. It would also mean having more buildings/town units to look forward to. Rather than just gatherer, you could have crafter + whatever you can think of.
I could probable do this all night so i'll leave it there