The content plugin support has always been a mixed blessing. It was sometimes useful as a stop-gap until the browsers supported some new form of content (eg. SVG, MathML, ...). With the removal of plugin support and acceleration of the death of plugins it means that new content forms will have to be implemented in all browsers, which seems wasteful to me.
So what we lose is the ability to display new content forms inside a web page which (imho) is not a big loss nowadays.
For the legacy sites (java applets for configuration or secure "VPN" access, flash for ditto) the backward compatibility has never been great: random applets required exactly JVM 1.4.x.x, flash only worked with FF version x, silverlight only worked with IE, etc. so I don't think the impact is worse than what would already happen. I hope that the developers of such solutions go for html5 replacements primarily, and if that doesn't work then downloadable stand-alone binaries (or even better: open source).