To each his own, lttp is definatly a fantastic game i beat it once hehe, however I have to say I found the 3D ones a lot more fun than it even if they didn't last as long.
Majora's Mask's story doesn't suck, a super powerful mask bringing a moon down to destroy the world is no worse than a super powerful caped goon using the Triforce of power to destroy the world, in fact Majora's Mask actually was more impending doom than OOT's story, that in a sense made it a bit more interesting! Majora's mask is darker than OOT.
Granted MM doesn't follow Zelda's traditional style storys where you actually have Zelda in it, but If i have to choose OOT over MM i'd probably choose MM.
I don't believe OOT flopped, if I remember correctly, it sold fantasticly well, it got in the world records for the biggest amount of pre-orders (dunno if it still is but it definatly did).
A definition of Flop is "To fail utterly", can you honestly say Any of the zelda games fall in that category? none of them have failed in sales or gameplay that badly so far.
I've played worse than OOT, Wind waker and Majoras Mask.