I think that's something that is quite impossible to measure. For some prog aficionados, "good composition" may involve the clever structural juxtaposition of the various sections of a multi-part suite. For others, "good composition" might simply involve well thought-out arrangements and clever interplay between simultaneous lines. What about songs that consist of completely free jams and have no real structure at all (which is a whole style in itself)? Is that bad composition? The nuraber of ways in which such a facet could be measured are innumerable.
Suffice to say, from a talent standpoint I think it's unfair to compare any two types of music that don't even have the same aims to begin with. Prog is way better when it comes to the long multi-part suite, and so it should be, as that's not even the aim of most indie music genres. Conversely, indie pop is way better than prog when it comes to 3 minute ditties...which, it goes without saying, is certainly not the aim of prog.