Johto. It’s a place full of culture and history, the people are friendly, and contrary to popular belief, most of the fauna—humans included—won’t actively try to kill you.
But seriously, anonymous, that depends on your tastes. Alola and Hoenn are popular honeymoon destinations due to their tropical environments and relatively low population densities, but some people prefer the charm of Johto, the culture of Sinnoh, the bustling populations of Kanto, or Unova … for some reason.
I admit I’ve never thought about planning a honeymoon myself, as I have no intention of getting married, so I can’t entirely claim expertise on the matter. My partner and editor, as I understand it, largely feels the same. But with all decisions, at least the two of us can say that you should think carefully about what it is you’d most like to do immediately after your wedding (besides, well, consummating it) and plan your honeymoon around that. If you’d like to lie on the beach or relax in warm environs with beautiful scenery, this would be why Alola and Hoenn are popular destinations. If you’d much prefer to do something on your vacations, Sinnoh has plenty to do if you’re looking for hiking or visiting quiet towns, and its sister region of Johto also has plenty to do if you prefer more urban environments.
Good luck, and congratulations, anonymous!
The Pokédex According to Bill 