Flash was also cancer that ruined web pages.

The reason Java Web Start wasn't, was specifically because once you clicked on the link, it downloaded the app and started it as a real desktop application, with its own window and taskbar entry and whatnot. It didn't rely on being embedded in HTML (I'm specifically not talking about Java applets, BTW -- they sucked too) or manipulating the DOM for its UI; it could use Swing and have the same look and feel as a native application.