What's Pepperflash? Will it still run Flash on a website, or it is some propriatory standard that no-one uses but Google? To be honest, as long as functionality is retained, I'm not too bothered. I mean, it's not like Flash is open-source, so we're not even losing freedom.
Chromium is open-source (BSD/GPL?), so there shouldn't be a problem re-packaging the code (Debian does it with Firefox, after all). I guess it would be nice to have a Chromium build without it, but as an end-user, I don't think I'd use it. Nice to have the choice though!