Yeah, Majora's Mask and Skyward Sword are my two favorite Zelda games. I actually consider A Link to the Past and Ocarina of Time to be better than Skyward Sword overall (although some specific gameplay elements are more refined, such as combat and puzzle-solving), but it did a lot of things I wanted to see in a Zelda game, so, that alongside of its overall extremely polished design, I couldn't help but enjoy the hell out of it.
As for Majora's Mask, I'm actually a huge fan of the time mechanic. I've never agreed with the complaints about it, although I can completely understand why someone would personally dislike it. Other than that, its sidequests are gripping, its puzzle-solving is some of the best in gaming, and the amount of attention to detail put into it is just mind-blowing, especially for its time. I'd easily argue that it's the most polished and engaging Zelda title as a whole, even if not in every specific area.
By the way, after playing Darksiders II, I absolutely have to have a skill tree in future Zelda games. It's just too damn awesome to not use.