What you are doing is exactly the type of thing I am saying is bad. You are hampering the growth of your cites, and gaining less commerce by cottaging ever tile. You are also losing out on tons of production from converting food to hammers via Slavery. A 2 food 2 commerce tile is pretty freaking awful if I must say. It takes for ever for it to grow your city to another population, and it provides almost no commerce. Now when I say that the CE is bad, I mean it is BAD. You will not have many GP to push yourself to key techs faster, nor will you have much production. This does not mean that cottages themselves are bad. They are very good, but you need to understand when, and where to build them. A purely grassland city with maybe 1 grassland hill, and no food does not want cottages. This city will be working 1 cottages for a very long time, and 2 for the vast majority of the game. While farming it will allow you to whip many units out of it, because a 4 pop city working 4 farms grows back relatively quickly, as it will have 6 more food than needed to sustain it's population. The problem I see with you is that you do not understand which city would be better for what, and because cottages are the only thing you know you put them every where. This is not good, and is hampering the growth, and research rate of your empire. You really only want cottages in a city that can grow onto them in a reasonable time frame, or in one of the 4 cities around your capital that are working cottages for the capital to grow them. If you really don't understand please try to post a specific here, and I will try to get back to you fairly quickly.