About routing: It depends on how you're planning to get your C seat. If you are going to pay for it, you can select any routing that fits you. However, if you are hoping to use miles to upgrade, it is a lot harder to do so for SFO - HKG and ORD - HKG than JFK - NRT.

I also find that food and services are a bit better on JFK - NRT than flights from ORD or SFO. This is just my own perception though.