Libtool recognizes and deals with many different compilers, but sometimes uses options that cause compilation problems.
For instance, libtool is embedding full paths in MacOSX shared libraries.At that level, libtool seems to ignore directives passed to it via autoconf/automake.
Already not possible to use libtool for VC++.
Provide additional build methods other than using libtool with autoconf. For instance, cmake is a good alternative, but it may not be available everywhere.
Consider dropping libtool altogether, which would mean being smarter about compiler names.
As of HepMC 2.06.06, cmake is the prefered build option.
Also as of HepMC 2.06.06, the Windows build has been dropped.