Musashi's new moves are a blast, but level design in Shinobi 3 kinda drags on without much in the way of excitement. Things get really fun at the last three levels, but I find myself laboring through the early levels to get to the good stuff. Revenge's levels are better but you really miss Musashi's ability to run, which puts a damper on your enjoyment, so you can't win either way.
Call me crazy but out of all the Genesis Shinobis, I like playing through Shadow Dancer the most, prolly cause it's faster-paced (albeit shorter) than Revenge or 3.
PS. Shinobi 3 pwned Revenge in the music department, sorry Yuzo.
PPS. Oh and Nu-Shinobi on PS2 rocks, from what I've played of it anyway (about halfway done).