It comes as no surprise that the location shots for the Mamma Mia sequel will not be be shot in Skopelos but in Vis, Croatia. See:
I’m sure logistics had everything to do with the decision. Croatia has provided locations for Game of Thrones for the last few years so the infrastructure, at least on the mainland, is in place to support the production. Skopelos doesn’t. Croatia will be way easier for the production crews.
Last year I spoke with the Set Designer for the original film. The designer told me that all the sets for Mamma Mia were constructed in the UK and hauled overland to Volos. There they waited and waited in July for space on ferry boats for their trucks to bring the stuff to the islands. A familiar problem.