Some of the buildings seem to have pre-requisites, or some other requirement. I say "seem", because I'm not really sure. I know in certain cases I can't build things, but unless its a resource issue it's really not clear why from the UI. This is especially bad when it's due to the settlement level, as the buildings won't show up in the list at all.

I'd suggest that all buildings you have the tech to build appear in the list, even if you can't build them. When you mouseover one, have a tooltip explain what is required to build it. That would make things a lot clearer.