There's a few things I've come across that I don't like personally, such as:
* Requirement jump from Citizens to Paticians is too steep.
* Having to chain market buildings so you can build on the other side of the island is annoying, they may as well just let you drop a market building anywhere on an island that has a harbour controlled by you.
* Milk and Pig farms radii are too small for my liking, they should be a little bigger considering the size of the pens and how annoying it is having to rebuild a large farm area to fit another couple in.
* You should be able to place "ghost" buildings which cost nothing and are 80% transparent which serve purely as a placeholder so you know the proportions of some buildings and can design areas. Would be especially handy for farms.
* I dislike how powerful Oriental boats are compared to the Empires boats, small empire trading ships should have an armament of 1 or 2 to balance out that the small Oriental ships get 2 "buff" spots.
* Hate when the game gives you quests for delivering an item that you cannot make, it should only give you quests that you can actually do without having to frantically try to build some buildings to get the quest sorted or ignore it.
* Should be able to rotate / refresh the honor stock goods at Northburgh and the Oriental guy, at a cost to Honor and it takes a while for the items to come back in. This means you can refresh and rotate the goods to get the items you need, such as I badly need some Coffee seeds and +% sailing speed sails in my game yet I keep getting things like +damage for boats (which is annoying when I have Corsairs and computer players turned off in my continuous game).
* I wish after exiting post card view it'd put you back at your original view, as in the original direction you were facing when you entered post card view.
* I wish the game had a far more in depth analysis and breakdown of the production figures for all your islands and populations.
But hell, I'm still having a lot of fun

It's a great game.