"How can this problem be solved?"
By saving the data in the MAT file as separate arrays, and not stuck inside a scalar structure. This has other benefits too, e.g. the ability to load/replace individual arrays from the MAT file, or accessing them without loading using MATFILE.
Use the -STRUCT option to achieve this. For example:
D.hello = 'blah';
D.world = pi;
save ('test.mat','-struct','D')
Now all of the arrays are saved separately, not in one scalar structure:
whos -file test.mat
This means the data can be imported directly into the output structure as you expected:
S = load('test.mat')
S.hello
S.world
