This is definitely the hardest part of any RPG. While not so much a traditional JRPG, I had the exact same dilemma when I started playing Culdcept Saga recently.
My default course of action when naming a character in any RPG is to just use whatever the system offers by default. When I played through Dragonquest VIII my main character’s name was Hero. This way when I talk to someone about the game its easy for me to say, “Remember when Cloud was riding the motorcycle.” Instead of “Remember when OchoCinco…I mean Cloud, that was his name…I think…was riding the motorcycle.”
My second course of action is a variation of Momus. You do know who Momus is, right? Momus is simply the greatest god in Greek mythology EVAR! Momus is the god of satire and mockery. So when I name characters they might be Momus, Momo or if a female Momiji.
Nonetheless, it is still the hardest part of any RPG: except for Final Fantasy XIII where the hardest part was just playing it.