It's the Zelda that Nintendo "rushed out the door" - in order to get it to market in 15 months, they reused the engine and mostly reused the assets from Ocarina of Time. That's quite well-attested.
My theory is that the short development time meant that they had to just go with it. The design team knew the tools, so all the content is pretty polished. They didn't have time to refine it all, so there's loads of stuff that is just plain weird. No other Zelda game has a UFO abduction section, but someone spent ages on it and it takes up about a tenth of the map, so fuck it, it stays in. That all gives it quite a "daylight horror" vibe, which is unusual in gaming - seems quite normal until you scratch the surface. The "groundhog day" conceit also allows for quite a few "bad endings"; most games wouldn't allow things to go so wrong, but since you can put it right, it's okay.
Less time for focus groups also means that there's less time for Aonuma and Koizuma's original vision to be changed. I don't think it's the game that Nintendo would have wanted to put out the door, but since it was the only game available, then out it went. Which I appreciate, because it's my favourite game out the whole franchise. It's unusual for Nintendo to put out something so dark, doubly-so at the time.
Obviously, fuck the down-the-well bit; that just wastes your time.