I don't know whether these where mentioned before as I didn't read the whole topic, but I found some inconveniances (just started playing today).
1. When building a tower, it has range of view before being built, so I can order it to be built, then stop and it is ultra-quick scouting.
2. The game is auto-saving even if paused for a long time, so it basically saves even though nothing could change in the game.
3. Everytime I receive infomation about productivity boosts, it boosts 0%.
4. When unit is set to explore, it will stop when all land tiles of region are visible. But there might be some blackened squares around which a priori are not known whether they are land or water, so theoretically they should check them too.
5. I have a feeling that bakeries produce food even if there is a slight shortage of wheat, e.g. having 1 farm producing 5 wheat and 1 bakery seems to constantly supply population of 9 (4 initial + 5). I am not too sure about this one though.
I like the idea for the game, but I think it requires too much micromanagement - I need to click each building several times to upgrade or to build (for bigger towns it is really boring), building roads between settlements take a lot of actions etc.