The native api isn't only necessary for accessing operating system resources or running natively compiled code. It's also to interact with the browser at a fundamental level. It's extremely useful for things that modify the user interface or need to interact with the dom, like vimperator, ublock, tab mix plus, etc...

I think one of the bigger problems with a non-native plugin api is that doing anything non-trivial could become either unnecessarily complex or possibly even intractable. I'd be curious how they are planning to support extensions like vimperator or even no-script.