System apps like Terminal, Disk Utility, Preview, etc. Yes.

Stocks, News, iTunes, Maps, Photos, Mail, etc, should be optional.

I think they mean that the stock apps should be updated separately to the OS, like any normal app

I guess I'm expecting system wide features that only Apple could add because they involving updating the underlying OS. Adding group chat to their video chat app that I never use for example isn't that interesting to me and shouldn't require an OS update.