Question of prior art, really. The reason the lawsuit for guitar controllers doesn't fly is the same reason that Harmonix is not suing Activision: the controllers involve substantial modification in functionality and design and thus are 'improvement over prior art'. Konami's Rock revolution stuff failed to distinguish itself in that respect and thus left itself wide open.
I'll use a hypothetical automotive version: company A patents single throttle-body injection, company B makes a per-cylinder throttle-body system. Company C makes a per-cylinder system that's electronically controlled, thus is an improvement and B can't sue them. A, on the other hand, copies B's per-cylinder system verbatim in revenge and gets sued.
Prior art is an INSANELY relevant portion of patent law; to patent something without establishing prior art and difference is likely going to get you thrown out because somebody else DID come up with something similar. It's guaranteed, your design is by default identical to whatever similar exists unless you lay out the differences and prove that you know what's already out there.