Well I mean it reminds me of an SNES title that only had a limited release in the West called Terranigma, but that isn't the game you're describing.
Still, terranigma is one of the greatest rpgs ever made. To the point where I've desperately wanted to clone it with better graphics. But its just not something you could market anymore. It was too hard, too cerebral, required a long memory to even advance and nearly photographic memory to navigate at points in time because you were creating, Earth.
To put it in a framework, The Legend of Zelda is a kids game. Terranigma is what serious gamers of that style were playing. It was even pseudo-3D.
To that end there are many old games that are astoundingly good even today, Terranigma is one. Secret of Mana 1&2 as well(albeit if you can't read Japanese the American versions are, childish). Final Fantasy VI deserves a reboot with 3D graphics, only side effect is that the game is so universally loved in Japan it could destroy their economy to rerelease it. Chronotrigger and Chronocross deserve honorable mention here. As does Ultima VI and Lufia 1&2. Just to name RPGs that you could play today and enjoy the hell out of for sixty to ninety hours. That's no joke or over exaggeration, some of these games take that long to complete.