Sega didn't make any PC Engine ports. Most have their developer's signature traits. It also doesn't make sense for Sega to make some things or the game overall better on PCE than Mega Drive.
There are lots of great Sega games and lots of great ports of them for PC Engine, like Cotton, Bikkuriman World, Monster Lair, Dragon's Curse, Dynastic Hero, Afterburner, Puyo Puyo, Fantasy Zone, Bonanza Bros, Columns and Outrun (popular opinion).
Decent ports which are good games: Space Harrier, Gain Ground SX, Puyo Puyo Tsu.
Shinobi turned out great considering it was done by Asmik. It may have cut some content, but I believe that it's actually ported pixel-for-pixel, which was ambitious for the time.