I am still on the shantae train, but she does have some stiff competition still.
Crash is both big in NA and JP, voted qell, and been on the upswing for a few years now, especially during smash development. I think he has a good chance.
Another namco rep of either tales of or tekken or soul calibur. All 3 are big main titles.
Another capcom rep most likely just being a RE rep(hoping jill), or MAYBE Pheonix Wright.
I dont think doomguy is that likely anymore mostly due to... well way too violent. That last gameplay sold me on that.
Only indie Shantae has to watch out for is Reimu. She is massive in japan and could be considered a bigger indie queen then shantae.
Ryu Hayabusa also has a fighting chance due to being the last unrepresented nes classic in the game.
Snk has Mai shiranui, the biggest female fighter in gaming probably(at least japan side).
Rayman also still has a chance, despite having a lot more spirits then shantae has. There are a ton still to pull from so its not like its impossible for him to have his own special spirit board.
If i missed anyone else big just let me know.
Crash, I already explained how he and his fanbase have to contend with Spyro, it's either both or none if you don't want a bloodbath.
I won't discount the possibility of those Namco reps, but I honestly think Reiji's role as the main protagonist of his own massive gaming crossover makes him such a good fit for Smash that it overrides the relative lack of knowledge about him from fans.
You say Doom is too violent, but you don't think the hideous mutated abominations with their exposed organs of Resident Evil aren't? I also fail to see what any protagonist can bring that Snake doesn't. You only have to look at Ridley and how he pulls off stabbing people in the heart, scraping their heads across the ground and crushing Mario's head in his trailer to see how they can pull off violent without raising ratings.
Reimu may be a hit in Japan but demand for her in the west is near nonexistent. Dragon Quest is even bigger there and even though it's appeal here may utterly pale in comparison, it's still a fairly recognizable brand by most.
And I have trouble seeing an SNK character due to their general lack of presence on Nintendo platforms. Plus you have to be pretty darn special to share Mr. Fighting Game Ryu's Smash niche of using special inputs, and I don't see Mai eclipsing someone like Chun-Li in popularity by such a margin it makes her a certainty. Not that it matters since they sure as heck don't factor genders heavily, otherwise we would have female alts for Hero.