I have an extension of pgfpages (imaginatively called pgfmorepages) which solves this issue, as well as extending the capabilities somewhat. The code is available at https://github.com/loopspace/pgfmorepages I'd be happy to contribute all or part of it to the PGF code base.
Check for node being coordinate doesn't use name prefix/suffix
node alias doesn't use the prefix and suffix
name prefix is incorrectly set with subpics of pics
\tikz@intersect@namedpaths persists outside scopes