I don't think either of those examples would really be a novelty character. I'd see them more along the lines of the Ice Climbers, where they're mostly just really obscure.
I lumped Mr. Game and Watch and R.O.B. together mainly due to age and obscurity. No one really thought they were going to be added to the roster. The same can be said of Wii Fit Trainer, but she's newer and well-known. How are you defining novel in terms of potential candidates and the two aforementioned characters? Many characters in Super Smash Bros. can be considered novel. For example, Zelda can transform and there are two Ice Climbers who are severely handicapped when separated or if Nana is knocked out. The Ice Climbers are novel
and obscure. Mr. Game and Watch and R.O.B. are both unique in their releases. Mr. Game and Watch hadn't appeared on a traditional Nintendo handheld or console (until the Gallery series). Besides cameos, R.O.B. was only featured in two NES games.
StarTropics has never been released in Japan. There aren't a lot of Nintendo games that can be said about. I don't think StarTropics was ever even mentioned in the trophies either. I'm not suggesting him out of fandom as I may have played the game a few times at most.
They're not that old and their obscurity can be debated, but the Elite Beat Agents can be considered novel.
It's difficult to think of a whole new obscure property they could drop in. Play as a Virtual Boy? Gameboy Printer? As was mentioned stuff like Mach Rider, Star Tropics, Takamura, Pushmo, or Chibi Robo are just low-profile as opposed to oddball.
After Mr. Game and Watch and R.O.B., I'm having a hard time thinking of characters in the same vein that work naturally, but there are no set rules to this. Neither Mr. Game and Watch nor R.O.B. fit into an easily defined category. For the purposes of this discussion, we're defining their common traits. The traits I've been using are: they're old, they were mostly forgotten, and they had unique releases.