There are probably people out there much smarter than me, so take this with a grain of salt.
If it were me, I would choose that my "main structure" should be a scalar structure - e.g. one simply called data. Inside this structure, you can then have multiple fields which can be other structures if you want, and each of these structures can be scalar or nonscalar as you choose. (You can also have cells, arrays, both of character and double, within all of these substructures). The primary advantage here is that a simple
Saves all your stuff. As well as that your workspace is not cluttered, since it only has the one variable.