Apologies if I've already replied here, I honestly could not remember doing so if I have XD
In any case... gosh, this is a hard question. For the underlying themes, the characters, the gameplay, and the other intricacies I learned about later, I'd have to choose MM hands down... but... I have to say that actually, OoT manages to win out as my favourite through, predictably, sheer nostalgic value.
You can blame my dad for this one... he never took much of an interest in MM, and never actually got past the 2nd dungeon... so as a consequence I was never that interested in it as a kid. But OoT, well, we would sit for hours together, tackling the dungeons one at a time until finally we were up to rescuing Zelda and saving Hyrule. I can't dispute MM improves and builds upon OoT in more ways that I can count, and once I played it later on and saw just how... deep the game is, I absolutely loved it. But when I came to type that as my answer, there was a little voice in my head reminding me just how much fun I once had playing OoT, and just how much I fell in love with that world and its characters... as cheesy as that just sounded. But that's the voice I have to listen to XD