The Messenger is next on my list. I'm currently on my second playthrough of Cyber Shadow unlocking the "feats", warming a little to it. But I can clarify my main gripes now.
#1, slow controls. We've had games with great player physics and tight controls since Super Mario, so it's hard to endure less responsiveness. It's like trying to play Super Meat Boy with Castlevania controls sometimes. #2, several levels involve waiting for AI and various moving level geometry for the right moment to proceed. If I wanted to sit around and wait for things to happen, I would go to the department of motor vehicles and read a book. As a ninja, I want to run and jump and slash and kill everything in sight. #3, lame boss fights. You're never really challenged to figure something out or react with good instincts. Once you learn the patterns, even the harder boss fights are a matter of doing the same thing over and over with few mistakes, like 8-bit Mega Man. I know that's true to form for NES, but it's not satisfying to me in a modern game. #4, music problems. It has glitches in timing between sections or repeats that sound like missed loop points, a distracting and sloppy problem. And it does not get you fired up to destroy. It sounds more like taking a drive on the highway.
It's still a ninja game, so I have to play it. Maybe I'll come around more as I tackle the harder feats. If only they had consulted me as a play tester...
Thanks for mentioning the other newer games. I'll check them out.