Ultimate Ninja. If it's even close to MNM of NGS2 then it's harder. S-ranking the entire game is piss easy if you abuse the game's features to the fullest. If you handicap yourself then it's about equal.
EDIT: this game isn't about difficulty as much as other action games. It's hard sure but not brutally so.
Start up R-01. Look at that ninja cat to your right, on the beach. Try hitting it.
Imagine that cat starting up a ninja dojo. If the cat is the master then NG3RE enemies are the students. They have their own set of rules.
Pretty much this.
From: rockman11_z | #003
I have another question. Which is harder, NG 3 RE ultimate ninja mode or getting highest score VR trophy?
It's a bit tedious but not too hard. VR18 is probably the hardest as you have to kill all enemy types without getting hit once as EVERYTHING kills you in one hit. It's pretty darn tense.
The biggest challenge you can get out of this game is it's handicap potential. You can really make up any type of run you want to make it as difficult as you so desire.
That said. MGR:R is fair, like God Hand. It doesn't play tricks or screws you over in any way to make it more artificial difficult like NG3(RE) does, like gimping Ryu of making his enemies ignore basic action game rules.