There is currently no way to fully implement something equally as good as the native controls offered by the OS. And this situation will not improve anytime soon.

It’s hard to create something good. Even implementations by the best teams suffer annoyances like buggy synchronisation of the timeline during playback or after scrubbing. I’ve seen this happen on both desktop and iPad on most sites, including YouTube.

Maybe even worse: some features native controls offer are just not possible to implement using HTML.

• Fullscreen: No standardised API for this yet. There is the FullScreenAPI by Mozilla (also implemented by Webkit and Opera), but as always IE runs behind the competition.
• Third party features: Most notably AirPlay on iOS devices. It is not possible to offer HTML controls to offer this functionality. Even if the standard add API’s for this, it will always be years behind whatever device / OS manufacturers have to offer.