>From the press release it seems NPAPI is OS dependent while Pepper is less so.
Correct. The NPAPI version of Flash is very platform-dependent; whereas Pepper Flash is almost completely platform neutral, and Chrome OS needs most of the same Pepper platform bits anyway. So, our maintenance overhead for Pepper Flash on Linux is very small. On top of that, Linux is broadly deployed throughout Google (and is very popular among Chrome developers), so we're scratching our own itch a bit.
Flash provides a lot of hardware abstractions, from H.264 accelerated video, to webcam and microphone access, and accelerated 3d (openGL) rendering. Does the Pepper API provide wrappers for all this stuff? Otherwise it would seem that Flash for Linux would still need to carry a lot of platform-dependent plumbing.