Something's off with the first statement. AeroMexico flight numbers 57 and 58 are nonstop services from Mexico City to Narita. I also remember there being flights that stopped in Tijuana in between. Not saying that there aren't any large countries without direct service to Japan, just that Mexico isn't one of them. Granted, AM57/58 seems to be twice-weekly, but if it took 3 days to transfer at SFO maybe it would have been a brighter idea to wait for AM58 to NRT (even if not starting from MEX, surely from within Mexico connecting at MEX would take less than three days?). I'm also in agreement with jib71.
The one thing I agree with is that now the government seems to be trying to get closer to China, as evidenced by the daytime slots that SHA-HND and PEK-HND have gotten and HKG-HND will be getting as opposed to the midnight slots that the US has gotten (however, they have the fifth freedom from HND as well as NRT; Chinese carriers don't have that at all, but it's not entirely out of the question since Korea now has exchanged fifth freedoms with Japan). However, how would the current administration have the power to do this "dramatic change" and not others?
(You'd be surprised how open some other Japanese bilaterals are- Japan-Macau is Open Skies except for Tokyo, as are Japan-Thailand and Japan-Korea; depending on how Ibaraki counts Viva Macau's attempt to open flights to IBR could very well only involve Ibaraki Prefecture because of their mostly open bilateral, just like Asiana's daily to Incheon; likewise, if Thai is facing capacity issues at NRT it can open up a flight BKK-IBR just as easily)