This is the game OP is looking for if they haven’t played it. The remake is great! SS2 is more build focused if they’re more into that and it can be modded easily with a lot of QOL changes.
Prey and Bioshock should be next if they haven’t played that.
I don’t think the 3DS is far superior at all. There’s nice QoL for sure. The change to Zora swimming to use magic was a dumb decision and the deku scrub water jumps feel terrible. Not to mention the whole game is brighter compared to the N64 version, which ruins the atmosphere to me. I like both versions, but the 3DS is more accessible, not superior imo. Here’s a good video about it if anyone is interested https://www.youtube.com/watch?v=653wuaP0wzs