Megaton:
Wasteland Explorer Theme: It's full of dirty junk from the Wasteland, which is what most of the houses in Megaton have as furniture. Somehow I can't see a resident of Tenpenny Tower having a broken park bench or motorcycle in their plush suite. I think this theme is good for Megaton because it matches the other houses.
Raider Theme: I have no idea where the heck Moira got the "decorations" for a Raider theme, but I think this fits Megaton more then Tenpenny Tower. If only because the Megatown house is a run-down old rusty shack which is the kind of place you can expect to find Raiders in the Wasteland.
Science Theme: Since the Megaton house is made of metal, that seems like an ideal place to build a labratory safe from the elements of the Wasteland to do your experiments
Tenpenny Tower:
Vault Theme: Adding this theme in Tenpenny Tower makes the home feel more like a Vault then Megaton. You get purified water in your toilet and the building looks cleaner then the Megaton House.
Pre-War Themne: I think this goes perfectly in the Tenpenny Tower home. All the other residents pretend to live in the Pre-War era and it feels more like an actual Pre-War house in Tenpenny Tower then in Megaton.
Love Machine Theme: The main bed gets replaced with the heart waterbed which I think is more fitting then having two beds in the Megaton house. Also it's set up in a clean room, which I think is a more ideal place for "bow chicka wow wow" then the rusty Megaton shack.