Is there a one-liner for creating the entire dataIwant?
Not using out-of-the-box MATLAB features, but you can overload the subsref method of the class to have any behavior that you want.
Why is this so slow?
It depends on many factors, such as the memory consumed by the array, your MATLAB version, whether you executed this from the command line or inside a function, whether you ran this once or many times (so that the commands could cache).
But the statements you've shown are not trivial operations. They build whole new arrays, and so require memory allocation and copying. You should consider whether splitting your middle layer across many objects is really the best data organization for you. It might be better to have a single object with an array of middle-layer objects, so that you can index like this
dataIwant(3,2) = topLayer.middleLayerProperty(3,2).bottomLayerProperty;
