You mean Revenge of Shinobi.
Shinobi III is only numbered as it is because it followed Revenge and Shadow Dancer on the Genesis, so the English localization team figured it should be labeled as the third in a series, while in Japan Shadow Dancer was considered something entirely separate; RoS was actually called The Super Shinobi in Japan, and Shinobi III was called The Super Shinobi II.
In terms of controversiality, I mention liking Shinobi III more than Revenge because among critics, Sega nerds, and those who generally get nostalgic about the Genesis/Megadrive, yes, Revenge is considered the better of the two. Among those people in particular, it's generally looked upon it with much more fondness than its sequel. I see it all the time in reviews. Not that Shinobi III is thought of in a bad light, it just isn't usually thought of with such rose-tinted goggles, even though it's clearly prettier, better-sounding, and better-playing than its predecessor (which is why it's on so many compilations; Sega objectively recognizes it as being better, regardless of nostalgic fan perspective).
On the subject of possibly controversial Sega-based opinions:
On a system that houses games like Contra: Hard Corps, Gunstar Heroes, and Alien Soldier, I readily consider Ranger X the best run & gun on the Genesis. Nothing else is as inventive or smooth in my eyes.
Also the original Golden Axe sucks ass. Alien Storm is way better.