Make each frame (not slide) appear in the PDF bookmarks with beamer

\makeatletter
\apptocmd{\beamer@@frametitle}{\only<1>{\bookmark[page=\the\c@page,level=3]{#1}}}%
{\message{** patching of \string\beamer@@frametitle succeeded **}}%
{\message{** patching of \string\beamer@@frametitle failed **}}%
\makeatother

adds the bookmark just for the first slide in each frame (or at least it seems to work on your MWE)