My concern with Shinobi Legion/X isn't much the "ninja cutscenes" with goofy sentaï-like jumps all over the place, this is kinda cool since its fits pretty well the Shinobi universe even if you're right, I prefer the darker presentation of the first installments and 2D sprites over digitized characters, for me the 2D games aged much better in term of presentation.
No the main problem with this game is the controls are clumsy, the level design is boring, the bosses are meh, the whole gameplay experience is clearly inferior to SMS/Genesis counterparts IMO.