I've been to Seychelles and the Maldives and to Madagascar, and the 1st two have little in common with the latter.

If you are the type of people attracted to Madagascar, you might find yourselves bored in the Maldives. I was ready to move on after a week at the Four Seasons. It's beautiful & the over-water bungalows are romantic, but I found the diving somewhat disappointing and there was nowhere to go out "on our own" to go exploring.

Madagascar is worthwhile, but do you really want to deal with potentially challenging conditions on your honeymoon? When I was there a few years ago, we found several romantic, but rustic, places to stay. Even in these places, the food options were very limited. After a couple of weeks of eating toast for breakfast & "chicken" and a (nicely presented!) rice mold for dinner, I did lose my appetite and some weight! Camping in a couple of the lemur reserves didn't go well; issues with the locally provided, falling-apart, equipment & we bailed on one place that was absolutely filthy. An organized tour would probably give you more consistency, but do you want to spend your honeymoon tagging along with a group?

I've always wanted to spend more time in the Seychelles; lots of different islands with different focuses & types of activities. It seems like a natural if you want to spend some time in a laidback, romantic place & also do a little exploration.