Two quick answers on that:
PDF annotations are an ISO standard since 2008. Paperpile honors this standard, if you annotate PDFs vie our beta annotator the annotations in the file in Google Drive can be read by any standards compliant program. Vice-versa, you can add annotations and they will be available in Paperpile. We will keep this with our new web-based PDF annotator and our mobile apps that will be released this year. If other programs ignore standard compliant annotations, there's nothing we can do about.
I hope you understand that we cannot officially or unofficially support any third party software for many reasons. We have ideas for the Desktop and offline scenarios but Mendeley (or EndNote or Zotero, ...) is not part of this plan.