In the geospatial software I'm writing and using these days, concerns are well separated. Fiona reads and writes features. Only. Shapely provides computational geometry algorithms. Only. Pyproj (not my work, but a favorite package) transforms coordinates between spatial reference systems. Only. The separation of concerns helps keep interactions between them predictable and as a user you pay only for what you eat.
A programmer-analyst's daily work has all the above concerns (and more, probably). A pip requirements file makes installing all three packages as easy as installing a single package like osgeo.ogr. I've uploaded one to GitHub: https://gist.github.com/1689767. This Gist includes an example of using Fiona, pyproj and Shapely together. Fetching them all, assuming you've got pip and the GDAL/OGR libs and headers already on your system, is just: