That's literally the one main somewhat valid use case for plugins, and it's basically because of DRM. A plugin that allows arbitrary code to run is a security nightmare, that's why we don't do it anymore.

A lot of the security features you describe were added by browser vendors late in the game because of how much of a security nightmare flash was. I was building web software back when this was all happening, I know first hand. People actually got pissy when browsers blocked the ability for flash to run without consent and access things like the clipboard. I even seem to remember a hacky way of getting at the filesystem in flash via using the file upload mechanism, but I can't remember the specifics as this was obviously getting close to two decades ago now.

Your legitimate concerns about JavaScript are blockable by the browser.

Flash was a big component of something called the evercookie—one of the things that led to stuff like GDPR because of how permanently trackable it made people. Modern JavaScript tracking is (quite rightfully) incredibly limited compared to what was possible with flash around. You could track users between browsers FFS.

You're starting to look like you don't know what you're talking about here.