MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I used Simplify3D, and there's an option called "dense supports" that does a few layers of higher infill supports where it touches the part. This helped a ton. I don't know if there's a similar option in slic3r...