Chrome's PPAPI version of Flash is now half the speed of the NPAPI version. This is purely unacceptable. In both using Stage3D and conventional Flash Display list, PPAPI lags miles behind in performance and doesn't even make use of hardware acceleration for Stage3D compared to NPAPI which makes full use of it.
My current solution is to simply show a small tutorial to manually disable Flash PPAPI whenever that version of the plugin is detected but it would be much more convenient if I could silently force the use of the NPAPI plugin in the background.
Is it possible?
There's no way to do this. If you found one, it would be a security issue and would be fixed, because if an attacker could silently force-switch a user from the sandboxed PPAPI plugin to the unrestricted NPAPI plugin, then the whole security benefit of having a sandboxed plugin would be lost.
(And hopefully your tutorial is pointing out to users that following your instructions increases their vulnerability to attacks from malicious websites, so that they are making an informed decision.)