Well, there are some debate about which version of MM is better, I would say 3DS is better but I’m biased because I have only played that version.
I also know about a restoration patch/mod to fix some new annoyances like the swimming mechanics (which were okay to me because I did not know better 😂).
If you talk about were to play it I did on original hardware, but since you are emulating a more powerful game, in with a think a bugless way, then you won’t have any issues with emulating this, on top of that you can improve the graphics, so if you don’t have the hardware I’d say go for it with emulation!