If you don't already own a 3DS, and you have the N64 version, just play that one.
The 3DS version did improve many things, like:
-graphics (many minigames and puzzles are easier to complete due to upgraded textures and crisper colours)
-time can be skipped ahead 1 hour at a time, instead of 6 like the original, meaning less waiting around if you have something to do at 11pm
-improved bombers notebook
-new 3DS has independent camera control with the c-stick (original you can only move the camera using the L button)
-added another bottle/bombers notebook quest
-bird statues provide hard saves instead of soft, single use saves like the original
-gyroscopic aiming (personal opinion); aiming on the N64 games was balls, and gyroscope made the Octorok shooting gallery 1000000x easier
-improved inventory management thanks to the touchpad (pretty much all the stuff OoT3D improved)
-2 fishing ponds (idk if this is really a positive, but I hear there's a secret boss or something in one of them. Never spent enough time in either to see though)
Some negatives in my opinion include:
-every boss now has a big weak eye to hit (annoying Zelda trope made even more annoying)
-Gyorg and Twinmold boss fights severely changed, Twinmold fight now takes 10 hours to beat
-a few mask locations have been changed, but if you haven't played the original you won't notice
Overall, the 3DS positives outweigh the negatives, I just don't like how they butchered the boss fights. The 3DS version is more friendly if it's your first time playing, but the N64 version is the first one I played and it's more than manageable for new players. I wouldn't say buying a 3DS just for MM3D is worth it, but the 3DS has a great library so the console itself is great to own. If you're short on cash, just stick with the Gamecube port. It's only slightly worse than the 3DS version, but you get the original, better boss fights.