In my opinion whenever rooms flow together so should the flooring or you run the risk of it looking like you couldn't decide so you picked them all. I would takt your love of tile and use it in the bathrooms and outside on the patio you can go crazy with stone.

It's fine to use stone and tiles in the foyer, bathroom, or kitchen area, but not the main living areas.

Really would like to know what you ended up doing...we are building and want to use cement encaustic tile in our bathroom and hardwood everywhere else. Our builder brought to our attention that the flooring would not be level because of the thickness of the tile. did you run into this?