Seems like most of my Sega-based mentions end up being contested (when I said Sonic Adventure 2 was better than the original, and saying JSRF was better than JSR), so maybe this won't seem controversial to some.
But Shinobi III is waaaaay better than Revenge of Shinobi. And the soundtrack is much better too, even without Yuzo Koshiro on it.
His best work wasn't even with Sega anyway (as most people seem to laud him for RoS and Streets of Rage, primarily). His best work was on Actraiser and the original Ys games. And Beyond Oasis is his most technically-impressive, in my eyes (making orchestral sounds with the Genesis sound chip and all).