Historically, plugin use was much more widespread, and there were plugins for all kinds of things. You had to have a separate plugin for each of Video for Windows, RealAudio, Quicktime, Shockwave, Java, etc., and there were others for playing different media types like .mod, .xm, .it, displaying image formats, ...
The NPAPI interface was also standard enough that every browser supported it. So yes, it's "more wrong" to add a new interface to new proprietary plugins than it is to continue supporting a dying legacy interface to proprietary plugins. The NPAPI trajectory was downward, while EME's intended trajectory is upward.
I think this needs data. From my foot in the enterprise world, this doesn't seem even close to true; random SSL VPNs and the like require Java. If anything, most people are running an out-of-date version of Java because corporate IT hasn't approved the one that fixes ten exploits yet.
> and Flash was only required for some video and animation sites.
Due, largely, to (EME-free) HTML5 video and other HTML5 features. EME is not replacing HTML5 video, nor is anyone talking about using EME to replace Flash-played videos that weren't using DRM inside Flash.
There's a lot of implication running around that Flash is being replaced with EME video. It isn't. The vast majority of Flash is being replaced with non-EME HTML5 features. A fraction that was previously implementing DRM in Flash is now implementing DRM in EME.
NPAPI plugin usage, specifically Flash video, was going to continue to be a thing for Flash videos that were using DRM. (You could make the argument that these things would just drop DRM if it were too hard, but given how long Flash stuck around until there was a high-quality replacement that was objectively better than Flash from the content-publisher's side, it's a hard argument to make.)