Not everybody has money. Even for a honeymoon.

I also thought about regional passes, as they are a great value cause you can use a few days over a long period of time. But they are regional and don't cover all these areas. If they are going through all these areas might as well get a JR pass, but that would blow the budget.

Honeymoons should be memorable. Just because you are not spending loads of money doesn't mean it is memorable. People may have a memorable trip taking an overnight bus, just as memorable as spending time on the beach in the Maldives.