I think our Civ4 tile-improvement preferences need to get together and make babies Muxec.
I find that I too often take city specialization to an extreme and end up with slow-growing, hammer-poor cottage heavens. I mean they can be as good as a gold mine! In every tile!
It was instructive to me to see what others did in the soon-to-be-concluded CEO Shaka/Hostile Takeover game (I know you have been following it, but any others reading this thread, I am referring to
http://forums.civfanatics.com/showthread.php?t=319150). To see places like New Riverside with a fairly even mix of farms, mines, watermills, and cottages definitely illustrated a way to balance city needs.
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To answer your question, it's certainly not difficult to make cottages. Just press "t" when you have a worker selected
Even some currently-playing SG's demonstrate that SE's and Hammer-Economies can work on higher levels, so I think to some degree it's a matter of preference and personal play style, which is how a game should be ideally. In my opinion cottages are just easier to use and don't really require that much micromanagement.