I think we've made the situation worse in releases 1.5.10+. For example, if you have GEOS installed on your OS X system, and pip install one of the batteries-included wheels from PyPI, the system's GEOS .dylib is going to be loaded instead of the wheel's .dylib.

I propose to largely roll back the changes made to setup.py, shapely/geos.py, and shapely/libgeos.py since 1.5.9. Then I will replace shapely/libgeos.py with a module that is only ever imported by setup.py. I'll feel a lot better if geos-config is never executed except when we're running setup.py.