Actually I meant an RPG actually published by Nintendo and the IP owned by Nintendo itself. True there were many RPGs on GBA but Golden Sun was by Nintendo!
And the request don't help that less, Little Mac is probably in due to demand and popularity.
Well the beginning plot is along the tropes of many JRPGs that the protagonist must leave his isolated home and go save the world and everything but the way game executes it is wonderful. And the way the story then develops is pretty different. Has some twists and turns but not too many. Although some are just surprising to be honest and the game has a really good story. Plus the role reversal in the 2nd game controlling the previous game's antagonists and the eventual reunion adds more to the story. Have you not played Golden Sun or forgotten all about it?
The Djinn kind of like Pokemon added more variety to the game. Basically they are the ones who boost your class, not level ups. So no matter how much you level up, your caps won't change much. But more Djinn will boost that class, upgrading your attack, hp, speed, everything. Technically if you don't collect Djinn, you would have a tough time beating the game. Plus each Djinn has a unique ability. You can use it during battle, such as hitting for high elemental damage, healing the party, boosting some stats, etc. Then the Djinni is standby, you lose your buffed levels and classes but the fun starts. You can now summon the Djinni to deal very high amounts of elemental damage which in turn also boosts your elemental power. Subsequent summons or spells of that summon will be strengthened. The more Djinni you summon, the more powerful the summon is with you summoning huge gods and deities by the end. And after the summon, the Djinn go into recovery mode. That is that the Djinn can't be used, neither does he provide any stat bonuses till s/he recovers. I haven't played anything else like it!
Plus the mixing of Djinn to get dual elemental and tri elemental classes is awesome!
I have played tons of RPGs myself and have yet to find something Golden Sun-ish so according to me its a fairly unique game. Combat is turn based, which Nintendo lacks, like Final Fantasy but not real time. Plus the view is of the protagonists from the back during battle unlike the side view of FF. And using psynergy out of combat to solve puzzles in dungeons as well towns is very different. None of the Final Fantasy or any other RPG have puzzles like that, just dungeons.
It was pretty unique according to me. I think many other people would agree on that.
P.S. I just saw the posts above that other people agreed with me and this is probably unnecessary but now I have typed all of this so posting reply!