I wouldn't count those crazy KOEI games (aren't they more like simulator games than RPGs?) but even if there were a few, games like Super Mario RPG: Legend Of The Seven Stars, Chrono Trigger, Secret Of Mana, Final Fantasy IV and Final Fantasy VI are still among the best RPGs even today. And there were several non-Square games or less common ones (7th Saga, Arcana, Breath Of Fire & Breath Of Fire II, Illusion Of Gaia, Lufia & Lufia II, Paladin's Quest, Robotrek, Secret Of Evermore, Shadowrun, Soul Blazer, Twisted Tales Of Spike McFang) which were a lot of fun, at least IMO. But then again even I liked Final Fantasy: Mystic Quest and played it several times and own it for some reason. >_> (I don't count The Legend Of Zelda: A Link To The Past as an RPG but it doesn't affect the list much either way for comparison's sake to the Genesis library.)
The Genesis did have more arcade-style games, but I chalk this up to Sega themselves being rather arcadey. Some games like Jurassic Park looked more exciting in the Genesis version than the Super NES version, or at least maybe because of the commercials. Commercials for Genesis games were often more interesting, though Nintendo got a little better when they kicked off the Play It Loud! campaign.