Bangkok is an awesome city to spend a night or two at either end of your trip so you can eat some great food and visit some temples, but I think you're making the right call to mostly avoid it for a honeymoon. It's really not as seedy as its reputation, though, unless you go looking for the seedy parts.
If I were you, I'd look into going to Koh Chang. It's a really nice, peaceful island that's only ~5 hours by bus/ferry from Bangkok, but it's the opposite direction of all of the other beaches that you'd want to go to unless you're thinking about going to Cambodia as well.
Northern Thailand and Laos are my favorite places over there, but that's more jungle than beach, so I'm guessing you're looking for advice on the islands in the southwest of the country, and I'm not much help there.
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