- Alien Soldier
- ALISIA DRAGOON
- Beyond Oasis
- Castlevania: BLOODLINES
- Contra: Hard Corps
- Crusaders of Centy
- Dynamite Headdy
- Ghouls 'n Ghosts
- Golden Axe II
- Gunstar Heroes
- Landstalker
- Phantasy Star IV
- Ristar
- Shining Force II
- Shinobi III: Return of the Ninja Master
- Sonic The Hedgehog 2
- Streets of Rage 2
- STRIDER
- Super Fantasy Zone
- The Revenge of Shinobi
- Thunder Force II
- ToeJam & Earl
Went through your suggestions and cut quite a bit. As much as I love SF2 Champion Edition, it's a multiplat and the SNES version has better graphics & sound (and on actual hardware, better controls unless you got a 6-button Genesis pad). Toejam & Earl 2 is fun, but a lot more "standard" than the original, which has more unique gameplay. M.U.S.H.A has great gameplay but the Sega CD version is better, and IIRC it also had a SNES companion game at some point.
I would've kept Pulstar in there but there's probably a bit too much overlap between it and Ristar, but if you could squeeze it in it'd be worth a playthrough. Kept all the Treasure stuff because their output was insanely varied and high-quality on Genesis/MegaDrive; even their McDonald's game might be worth a peek for curiosity's sake. Cut out Earthworm Jim & other multiplats because, well, they're multiplats and in a lot of cases the SNES version was better in areas like visuals & sound. Original SOR was cut because the sequel makes it pretty much redundant IMHO. Phantasy Star IV is a must-play; basically the best JRPG on Genesis/MegaDrive. I guess Shining Force might be worth checking out, but Shining Force II improves on its gameplay quite a lot.
Crusader of Centy is a high-quality LTTP-inspired game, it's basically "what if LTTP was on Genesis"? Could be called derivative tho, that's why I also left Beyond Oasis in there; it's Zelda-inspired but a much more unique theme & setting. Shinobi-wise I'd also recommend Shadow Dancer on top of Revenge & III; it's kind of like the arcade version but has some twists in its own way. Not as heavy on exploration like Revenge or even III, tho. Bloodlines might feel a bit clunky at first compared to Super Castlevania IV (no diagonal whip for starters), but it's very fun and has a lot of variety, and good challenge. Hard Corps is the only Contra on Genesis IIRC, but it's high-quality too. The Genesis port of STRIDER is one of the best versions, and great representation of 3P during the early Genesis years.
If you want some additional recommendations, I'd go with Gaires (Renovation; side-scrolling shmup with great music & cool bosses), Aladdin, and ThunderForce IV, off the top of my head.