Flash performance under Linux is pathetic as it is, so It wouldn't bother me if Shumway ends up being 2x as slow. Flash is pretty much legacy at this point anyhow, so the only reason for a Flash implementation is going to be legacy support for sites that don't get updated. In a few years, the performance won't matter so much anymore. The platform independence and relative future-proofing of a js implementation makes it well worth the tradeoff in my eyes.
Then again, Flash performance is so aweful it also wouldn't surprise me if Mozilla's implementation ended up being faster, just because of how shit the Adobe one is.
There is a lot of flash video content out there, mandated by the copyright owners for drm reasons (unless they mandate the dreaded Silverlight, like Netflix). For Linux users, the real bottleneck is that the flash on linux doesn't do hardware acceleration. Since shumway uses the ordinary backends for rendering, the gstreamer native backend is available which indeed is hw accelerated.
So, perhaps we'll be able to watch flash videos under Linux without CPU decoding before flash is replaced (the hls encoded streams must also be handled...) I don't really see any other realistic alternative by now.