Love 'em both.
Majora's Mask is better designed, though, no question. I suppose this comes from the fact that pretty much all of the quests in Majora's Mask have an effect and you can't save everyone, while in Lightning Returns it's based around the opposite idea: you can save everyone. This would be fine if so many of the sidequests weren't simple busy work and you actually cared about the characters affected by them or what their dilemma actually was. Oftentimes you'll just do the sidequests because they're there, but the quest design and the actual dilemmas oftentimes aren't even that interesting.
MM, on the other hand, uses its smaller setting to its advantage and makes it pretty clear that most of the quests have major effects on the people involved and, likewise, you'll likely end up undoing it. So I'd go with MM on that basis alone.