I'd like a Metroid Maker more, that'd be sick. But I can't see either happening, these are expansive games that rely on expansive levels and interconnected areas, I just can't see Nintendo doing it. It's easy with Mario because the series is based around short, standalone levels.
I'm with you on wanting a Metroid Maker, but I absolutely agree with your argument against it. A Metrodvania is a well crafted world and a simple tool set wouldn't allow for the kind of nuance that would be required.
I'll go ahead and share my vision for howI think a Zelda Maker would work.
Imagine the original Legend of Zelda. The map would remain the same. This map could be rendered in the NES, GB, SNES, Phantom Hourglass, and New Link's Awakening styles. It would be up to the user to decide where to put each dungeon. They could be placed in random bushes, under boulders, or by walking into a fake fairy fountain, for example.
Each user could create individual dungeons for finding key weapons and tools in the game. These would be randomized into the locations on the main map, or you could create all of the dungeons yourself, or you could have a group of designers make them.
I'm not saying this is a perfect idea and that it isn't a little wonky, but it could be a lot of fun. Making sure that there aren't dead ends in the game design would be very key, but I think each dungeon would have to be able to be beaten by the user, and the entire overworld map would have to go through the same checks and balances, perhaps with just a simple AI test.