I think a button to activate a "map mode" that gives the ability to click somewhere in the village to teleport there in villager mode would be a cool feature, so we don't have to run a mile and a half from the starting house to see an area we just created every time.
I'd like to see visual upgrades for houses/mansions, as well as the other buildings. Start with wooden buildings and then upgrade to brick, stone, or other materials. Also, it would be awesome to be able to tell the different buildings apart. I've noticed that the fishing port creates more docks in the ocean and that building more farms creates raised earth near the ocean. These are great features and I'd love to see it used on the rest of the structures including the merchandise buildings.
Another thought for leftover knowledge points would be three different shrines (or like structures) where you could employ villagers to worship. Each shrine would be to the three resources (wood, stone, metal) and would increase the speed of resource collecting by a small set percentage. And as you upgrade the shrines, they can employ more and more workers to make the collecting bonus even higher. That would definitely put good some use to those knowledge points.
I think leftover knowledge points should be able to be used for things like reducing the time of the market update, increasing the selling price for items your villagers create for more gold, etc.