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.
Thanks to the digitized grapics I find that some bosses look pretty intersting in the shinobi universe.
Also some enemies look pretty bad like the snake etc but I personally find it pretty funny it gives it some charm just like the bad ninja movies from back in the day.
Furthermore The AI is smarter in shinobi x than in the genesis counter parts.
Also they if I am not mistaken shinobi X has one of the more difficult final bosses in the shinobi series.
I disagree with you on everything aside that 2d grapics age better.