Both great games but out of the 2 i would say i prefered MP3, even though it is a bit short. Both games do feature a bit of backtracking at times.
Zelda TP is a third person adventure mostly made up of exploring with a fair few puzzles. It should probably take between 40 and 60 hours to complete on average.
MP3 is an first person adventure involving quite a bit of shooting and a few puzzles. It should take between 12 and 20 hours to complete.
You could always get a VC points card and get both N64 Zelda OOT and Snes Super Metroid. Although their styles have advanced a lot the basic game mechanics are still pretty much the same so it could give you an idea which you would prefer.