>>12
Chrono Trigger has an "active" option, though both wait and active have little difference. There are some Genesis games that fit as well, even though platformers and sports games dominated it.
Ecco the Dolphin and its sequel, for example, are something of an RPG, though definitely not traditional in any respect. Toejam and Earl and its sequel are RPG-esque as well. Neither of which is top-down though. Both have platforming elements (Ecco's being less obvious for obvious reasons) and are more like Zelda in that the enemies are everywhere and you simply engage them if you choose to do so.
I haven't played any "classic" RPGs on the Genesis, but newer consoles were out by the time I got ahold of mine.