Definitely try Landstalker. It's like an isometric Alundra, but far better. (there's a sequel on SNES, but it isn't translated...)
Admittedly it is lacking...so I guess you kinda have to fiddle around til you find something you like. Sword of Vermillion is often praised but I can't stand it. Ditto the Shining Force games (they're more strategy than RPG, anyway). Come to think of it, I think even the SMS had more RPG's than the Genesis...Wonderboy in Monster World is often thought of as a RPG also, but it's also platformer. Everyone loves it, I think. Actually, I think the Sega CD even had more RPG's. Rent-A-Hero might be a RPG, but there's no finished translation and it's one of those games that NEEDS one. Super Hylide is a RPG, but it's on NES too as Hylide 3 I think...Sorcerian is loved in Japan, but not on Megadrive...there's The Story of Thor. I forgot that one. That's in english, too. I never played it much but it's well liked (perhaps only cos' it's a RPG on Genesis...). That's all I can think of, sorry.
Seriously though, Phantasy Star 2 and 4 are great. 3 is okay, but 1, 2 and 4 would stack up to be one of the greatest RPG series' of all time. If because of nothing else, it's because 2 had an ending worth seeing - a rare quality in RPG's if you ask me. It seriously changes the way you look at the whole series...
EDIT: I forgot to mention PS3 has 4 endings, and some of them make it even more...of a paradox. I guess.