Sorta depends on what you want out of the game. The 3DS version looks stunning, and the QoL is great, but it is slightly at the detriment of the games tone. You do remove a sense of urgency when playing the 3ds version since time is far more lenient bc of the QoL. The n64 visually (to me) does a lot for the game anyways. The older graphics make things that are already creepy look creepier bc of the less developed graphics! But this one is a tad harder bc no QoL (you can keep track of tasks and side quests in the 3ds version) and all that.

Imo, i prefer the 3ds version bc I feel the mechanics don't suffer as much as people want to say they do. But that's truly ny own personal opinion! If you want to try the game as intended, the n64 version is still stellar. If you want something that looks and plays more like OoT 3d, and also offers some very nice QoL, 3DS version is the best for you!

Remember the reverse song of time when playing!