I've played Majora's Mask twice, I loved it, but at no point did its saving mechanic feel like a challenge or nuisance. Getting to the save point was never a challenge.
The idea was that if you start playing, you have to more-or-less accomplish something in that save. Once you played the song of time, if you didn't have a key or a special item, you would have to get it again. That doesn't change with adding new save points, you still have to complete your goals within the 3-day cycle before playing the song of time.
Now, with the 3DS version, it just allows you to save more frequently in the middle of the 3-day cycle.....which I can't imagine being detrimental to anyone's experience. It just means casuals can play in smaller spurts, which we can all handily ignore.
This is like when people got upset over the god-mode in Donkey Kong and Mario. It was optional and clearly for gamers with less skill, but easily avoided and ignored by the likes of us.