As far as animations go, I do have to say that a Mortal Kombat character wouldn't animate any worse than some of the other strangely animating characters on the roster like Steve, Mr. Game & Watch, Wii Fit Trainer, and Kazuya. In fact, I'd say Kazuya is a good example here because he's an otherwise normal looking character with deliberately jank animations that mimic his home series. A Mortal Kombat character would probably take more liberties than Kazuya did, but with how characters like this are handled, I have a feeling they'd make them evoke the early games' style where all the sprites were just images of real actors. The actual animations will probably be smooth like the other characters, as I doubt they'd hand animate them, but you'd still get the sense that the character is animating as if they have real life physics while performing inhuman/physically impossible athletic stunts and animation cancels and such.
And then their victory and Final Smash animations are one of the smoothest in the entire game because NetherRealm's cinematic animations are Hollywood movie quality. In the context of Smash, this disparity will never not be funny.
EDIT: I just had an idea of you could incorporate Fatalities into Scorpion's kit. More specifically, his Final Smash. Initially, all it does is give you the Trophy Stand item from Super Smash Bros. Brawl. If you hit a fighter with it, it will do the iconic "FINISH THEM!!!" thing, and pressing either attack button near a fighter gives you Scorpion's classic Mortal Kombat Fatality. With motion inputs though, you get a cinematic version of it where it zooms in on the trophyified character heating up until it explodes, K.O.ing them at 100+%, and taking you straight to the win screen if they're the last opponent on their on last stock. This would be a fun way to get as close to gore without actually going there, and would sell the brutality of Mortal Kombat in a unique way. It also allows you to add other fun Easter Eggs like Friendships that do no damage or take stocks, but do still win you the match in 100+% last stock situations, or animalities where they have a T-Rex bite down on the trophies and shake them around like a dog with a toy or something along those lines. I don't know enough to say that this would work for characters other than Scorpion, but I think it would be a pretty fun and creative way of encorporating the Fatality system.