I think @aoudad’s suggestions on emphasis are sound, keeping both ease of reading and backward compatibility. On the rest, I tend to agree with @jgm. However, the bit that I find toughest to get behind is getting rid of shortcut reference links. Those are not only convenient, but are very readable as well. [foo][] gives up a bit of that human-readability for parsing convenience.
At any rate, looking forward to CommonMark 1.0.