Anyway, he said that the problem with Pepper is that its API is gigantic and its only spec is the implementation in Chromium. Other browsers could port the API but it come at very high cost due to WebKit-specific glue code.
The "problem" with pnacl is that it means the end of Javascript's death grip on the browser, which Brendan Eich is interested in extending for obvious reasons
To be clear, there are two things that have historically been called "pepper". The first was a basically a better version of NPAPI, with the limited scope that implies. That was replaced by something that's basically a Google-proprietary replacement for the entire web stack, with both the scope and the problems that implies.