Starting with Kodi 16.0 the USE flags for audio visualizations (+fishbmc, +projectm, +waveform) have been dropped silently, without any elog notice about the changed behavior. As a result Kodi is running without any audio visualizations. Apparently the configure switches have been dropped upstream, as they are supposed to be replaced by separate addons. On Ubuntu the Kodi team now provides official addon packages (kodi-visualization-*) instead. Before 16.x hits stable, these visualizations should be made availabe again - either through separate ebuilds or through the kodi ebuild itself. Maybe the USE-flags could even be reintroduced and pull in the matching kodi-visualization-* ebuilds (once they exist). This way the upgrade path would not break, but I don't know if that would be considered good Gentoo style :)
I'm working on getting the visualizations and other binary addons added to portage in bug 555792
