In a (classic, non-appified) native application, the application can do whatever it wants with your computer and your personal files, and only the OS' privilege

In a (classic, non-appified) native application, the application can do whatever it wants with your computer and your personal files, and only the OS' privilege escalation mechanism is stopping it from modifying system files (but will happily let you proceed if you sudo or click the windows UAC prompt). Vulnerabilities aside, at least Flash runtime didn't give unfettered access, and was even nice enough to ask for permissions to the webcam and microphone. Furthermore the runtime was frequently updated and patched by the vendor, and Flash being embeddable in web pages made keeping up-to-date individual Flash applications easy, as they were hosted on the server.