JS has different scripting engines and different dialects, so it isn't really platform independent in the sense that the same code will execute the same way on every computer. In fact, it's possible for JS to execute in different ways on the same computer when you run the code on browsers with different engines. There are plenty of instances were a page will not render the same way in different browsers (although this is usually because HTML use isn't consistent).
> That "half speed" number was the status as of a few months ago, and is still improving.
It's still an effort to reinvent the wheel. When a 1:1 ratio is reached, you (not you in particular) will still have ended up spending time implementing a feature that already exists on your OS, instead of improving the original program. For example, browsers have pdf readers baked in. Now you have a dedicated pdf reader on the desktop, and a slower, buggier pdf reader on the browser.
The problem is that programs on the desktop don't communicate well with each other to get the same kind of integration you get on a browser, or the underlying OS doesn't include programs to implement features that you want to include on your web page. I understand that it may be simpler to turn a web browser into a mini OS rather than get OS authors to change their OS (the Chromebook is a misguided attempt to take this to its logical end), but it is still an ugly and redundant solution.