Win9x didn't have the app store with a sandbox, one click to install, and auto-updates. If you installed a Python or a Java app without having the corresponding runtime, it just didn't work. If you had the runtime installed - which had to be done separately - and then later the user tried to uninstall them, they wouldn't get any warnings, but all apps relying on them would be broken. Not to mention versioning.
Think of it more as a Windows version of apt-get.