1) Is definitely the best idea there. I would think it would be more light hearted but it is a really cute and original idea. Have you ever seen FMA? I would imagine a tone similar to that. x;
2) This is a neat idea. I wouldn't turn her into the demon overlord but thats just my preference? Maybe turn her into stone? Its just that by turning her into the demon overlord you would have to introduce demonology into the world's lore and that might be a pain in the butt. Also while you can make cool mechanics i dont see this being an RPG (which is something you may be shooting for). I think things like battles would seriously break up and emotional tension you may have. Not only that, I would only expect those two characters in the party and no one else. How you would handle that would be interesting.
3) This is a neat idea but it would be hard to do in 2D. Furthermore I wouldn't expect this kind of game to be an RPG. Its a decent brainstorming idea though.
4) Have you ever heard of the Nobunaga series. Its a series of games where one country takes over all the other countries. Its more war based and is a tactical game. The recent addition to this was pokemon conquest. http://en.wikipedia.org/wiki/Pok%C3%A9mon_Conquest
It would probably be hard to make a serious story with this idea. Which is fine as long as the gameplay is great.
5) I like the robot part i just dont like the 4 heroes part. It sounds kind of dorky/cheesy which may be what you are shooting for. A better idea (imo idk if you care or not) would be you are the robot and the scientist has taken over everything and only you can stop it. Obv its more generic but i think it would be more appropriate for a theme. You could even create a dystopian world where people live in fear. IDK. Just trying to brainstorm and spark some ideas.
All of these ideas are interesting!