As someone that lives in Japan here is my advice -- forget about arrival airport -- HND may be a bit closer (time wise) than NRT but it's not a big enough deal to change flights....

Both ANA and JAL have FAR superior soft product (food, service, drinks) -- only because UA is pretty awful. Hard product in PE is equivalent, but I would give a slight edge to UA here... I do think UA is easier to upgrade to Polaris from PE than either JAL or NH with miles and money.... If you value pleasant service and food choose NH or JL -- if you like to play the upgrade game choose UA -- you may end up with Polaris lounge access and a great seat....