First I would like to state that I am not an engineer, and that any sensible person would get a licensed engineer to create a green home design appropriate for the window and seismic loads relevant to their region.
We do have a lot of experience building houses on expansive soil in the San Francisco Bay area. The common complaint we have in this area is that windows and doors open during one season and not during other seasons. As you stated correctly, the problem is caused by the house moving, not as one solid unit, but as if on a very slow-motion roller coaster, and the result is a shifting of some parts of a house relative to other parts of the house.
The main problems with this type of movement are the already mentioned door and window opening and closing problem, foundation cracks, drywall and siding or stucco cracks and flooring separation. As you can imagine, there are basically two ways of fixing this problem. Each of them have numerous ways of achieving these fixes.
The first way to stop this differential movement is to put the whole house on a thick (12-18") solid structural slab. This is essentially a large concrete slab that is so thick that it can hold the mass of the entire house without flexing significantly, such the independent of the movement of the underlying soil, the base of the house is all on one flat, though not necessarily level, slab.
This way of building the house is the easiest, though all that concrete has an amazing amount of concrete and the associated greenhouse gases associated with its production.
The second manner is to install a pier and grade beam foundation. This involves installing a thickened stem wall foundation around the entire house, in our area 12" x 24", with 4-#4 rebar, wound 12" oc. with 1-#4. This grade beam spans the space between piers, made usually of 18" piers of concrete, with similar rebar reinforcing as the grade beam, at 5-10' oc. These piers are deep enough to penetrate the expansive layer of soil, typically 8-10' deep here, and the through direct bearing on the bottom of the piers and frictional loading on the sides of the piers, supports the entire mass of the house, while isolating it from the expansive soil under the house. This is much more expensive than the mat slab foundation talked about earlier, but can be done on varied building sites, including slopes. The main challenge to this is the engineer. We have encountered engineers that demand piers 5' oc and others that are ok with 10'. Obviously, 5' oc costs twice as much, for twice as many holes.
Either way, get a civil test to determine the nature of the soil under your house. They usually do a drilling to get soil samples, send it to a lab to get characterization of the soil and then the civil engineer writes a recommendation to the structural engineer, defining how the foundation for the house shall be built. In our area, this costs $2,000 or the civil engineer to a typical house, plus $800 for the boring/drilling.