Depends on the kind of Japan experience you're looking for. Iwakuni is also nice, albeit in a different way.
Iwakuni is the Lemoore of Japan. Yes, the sushi and ramen are infinitely better than what you will get in the States, but it will be at a cost of living on a Marine base, with stupid Marine Corp rules.
Taking Iwakuni over Atsugi is like taking West Virginia over living right outside of New York City. I guess if you're a cyclist or motorcyclist then West Virginia would be cool too.
In all seriousness, Iwakuni will still be a cool opportunity, but not living just outside Tokyo cool.