it was an entirely shoddy game even by n64 standards.
Far worse than the quality of Aidyn Chronicles is this phrase right here, this is one of the most terrible phrases to exist on the Internets and I am so sick of seeing it. This passive troll phrase implies that all games on the Nintendo 64 have a lower level of quality than those on other systems, even others at the time (PlayStation and Saturn). In my personal experience I have found this to be far from the case; there are some far worse games on the PlayStation, even worse than Superman 64 and Carmageddon. People are so quick to forget this of course because the popular or "cool" thing to do is bash Nintendo. Although, I suppose Nintendo kind of brought this on themselves since they claimed to go with the "quality over quantity" approach and some people expected every game to be incomprehensibly awesome.
Anyways, I agree that Quest 64 wasn't bad by any means, and I think that the cold reception it received back in the day may have been more due to people expecting it to contend with the likes of Final Fantasy VII, which was an unrealistic expectation if you ask me. It's interesting that you mention one game had what the other didn't, because I feel that if both Quest 64 and Aidyn Chronicles were combined, it'd form a quite capable RPG with an interesting battle system and compelling story.
What about Paper Mario? I'd consider that an RPG, plus it was actually good.
Mystical Ninja is pretty awesome, but I myself don't consider it anything like an RPG. It's more like a cross between a Mario platformer and a Zelda adventure, with a bit of Japanese quirkiness mixed in for good measure.
You're not missing out on anything by not owning Ogre Battle 64. I just couldn't get into that game because the battles are so incredibly boring.
Another game with "RPG elements" is Harvest Moon 64. It's a farming simulation but there's also a small town you can visit, build relations with the people there, and progress through a storyline. You also level up your tools through repeated use.