Hard, epic and in 3D!
Story: I can't really make a comment on this because i haven't played any previous Shinobi games but i must say i liked the animations in between levels. I don't know how he got from feudal Japan to a futuristic city either.
Graphics: Best you can expect for a hand-held console but in my opinion it looks better in 3D. Sometimes it's difficult to see everything happening because of the scale of the view but that may well be my crappy eye sight.
Difficult: This is what got me. I had a very hard time learning all the controls and stuff to get through the first level :P. Even though i selected easy, i still die in every level a few times before i proceed. Summing up, this game is hard.
Controls: Once you get the hang of it they work quite well and don't feel awkward at all.
Levels: Each level is unique in its own way. However they can get a bit repetitive i.e. enemies throwing stuff, you dodging and repeat. That being said, i find the level bosses unique and it's fun to try and find their weakness.
So in conclusion i give this game an 8.5. If you have some spare money around the place or are looking to expand your 3D collection i say buy it, but try not to bust your 3DS due frustration :P.