>>712784231 (OP)Natively? The 3DS port had a better framerate, Iron/Hover Boots being itemized, and the characters closer resemble the illustrations from the N64 instruction booklet, mostly give and take with other visual changes though. Gyro aiming worked really well, and getting Master Quest to go with it is nice. Would be happy playing either version, however.
MM3D on the other hand changed a lot of shit for no good reason, but thankfully it has a fan patch for that. It has some cool texture work in places but also has things like glowing water.