Shinobi (arcade), Revenge of Shinobi, Shadow Dancer (Genesis) and Shinobi 3 walk all over buzzy ol' Ninja Spirit. Why do I call it "buzzy"? Because the music sounds like it is composed of primitive buzzing sounds.
Walks all over? Joe, this is the post the prosecutor will refer back to when the court forces you to enter drug rehab...
I hate to say but I do feel that Shinobi 3 is the superior experience. Ninja Spirit is an excellent game, but it still retains Irem's signature arcade feel, whereas Shinobi 3's set pieces/level designs and frequent boss/mini boss fights give it the feeling of a much more fleshed out game. Despite the life meter, there are still many cheap deaths to be had, giving it a similar arcade feel. Overall, in my opinion, Ninja Spirit is the best ninja arcade game, whereas Shinobi 3 is the best ninja action game, period.
People usually like one and love the other, so I'm not surprised that you have a preference for Shinobi 3 over Ninja Spirit. Personally, I like them about roughly the same, as games, but I like the overall format of Ninja Spirit a bit better so I give the edge to Ninja Spirit. It almost feels like Contra - Feudal Japan Corps. Which, to me, is a good thing. Both games have beautiful graphics, nice music (Joe Redifer is on meth), and brilliant gameplay. I just like Ninja Spirit ever so slightly more due to the fundamentals of its gameplay mechanics.
I just find it interesting that an 8 year old kid, with no exposure to any of the above, also picked Ninja Spirit.
BTW, I had him try Rondo and then play Castlevania IV. The giant rock men on lv1 of Rondo and the wyvern boss were giving him fits, then he seemingly breezes right through CV4's first level and beats the horse stable boss. He picked Rondo because, "It's really hard, and I like games that are hard and frustrating but not annoying."
I also had him try Mercs (Genesis) and Bloody Wolf, back-to-back. He said "both are cool" but he liked Mercs better because it had a "wavy flamethrower" and "more vehicles". Then he tells me with all the parachuting guys in Bloody Wolf and how the bad guys twirl off into the distance when blown up, they should have made the music 'It's Raining Men'.... BAHAHAHA