As frustrated as I am with AC of late, I think the OP's issue is as much a reflection of ANA's domestic policies as anything. My wife and I recently (Feb/Mar) has an all-NH coded-and-operated itinerary (YVR-HND-NGO, NGO-FUK, HKG-HND-YVR); and for both of the domestic Japanese legs we were unable to check in until physically at the airport. This meant in both cases, we were assigned middle seats in different rows; hardly a 5* experience. Given that experience, I'm hardly surprised the experience when codesharing isn't any better.