As others have already touched upon, you could certainly make Scorpion work by dropping all the major MK elements and leave him as a fire-bending ninja. The issue is that it's Scorpion.
The DLC characters like Cloud, Corrin and Bayonetta were polarizing to the fans due to people being salty over "x" character not getting in over them. Or "x" wasn't deserving for "y" reason, etc, etc.
MK is polarizing to the general public as a franchise. That's what PsychoJosh was trying to get at.
Even with characters like Snake and Bayonetta who have pushed things before, I do think a series like MK is where Nintendo would draw the line. Bayo and MGS are violent, but no where near MK's levels, which as a game , revolves entirely around it's hyper violence & gore.
If they stripped Scorpion of everything that makes MK MK, he wouldn't really be a good representation. But even with that as an option (as we've seen in Injustice) Nintendo likely wouldn't want to associate their brand with the MK series. Not to say they wouldn't ever have MK on their platform because they've had it in the past. I just don't see them being ok with Scorpion going toe to toe with Mario.
Sakurai already had trouble getting Snake to choke characters, but the stigma with MK I feel is too great in comparison to Nintendo who is more and more trying to preserve that squeaky clean image. Perhaps I'm looking into it too much but I think it's somewhat telling that Smash was brought down from a T to an E10+. Plus all the other censorship to their own titles in recent memory.
As for Ryu Hayabusa, I'd be down for that. He's one of my most wanted third-parties at this point, and I feel he still falls in line with Snake and Bayo. Tecmo Koei has always been on fairly good terms with Nintendo, especially now it seems with Hyrule Warriors, Fire Emblem Warriors, the co-ownership of Fatal Frame, etc. Heck, I wouldn't mind Kasumi as a second rep if they were to get two characters.