I actually did not find a problem with the save system. In fact, I actually found it better in most cases.
One example I use with this statement is the use of this saving system would have to be in the numerous side quests. Usually, in OoT, specifically the Biggeron Sword quest, you would have to restart from a certain point if you saved and quit. In MM, all you have to do is go to an Owl Statue, then resume your side quest without any trouble at all. This is helpful in 3-day side quests like Anju & Kafei or the complex Business Scrub trading sequence, as well as trying to do different things in Romani Ranch in the specific period of time.
The only objection I have to it is when you go back in time, all the puzzles and side quests reset, which isn't a great thing. In OoT, if you saved during the middle of a dungeon, it would retain all the puzzles you completed. Then again, in MM, the puzzles would also remain the same. However, if you messed up a puzzle and messed up the temple (Not sure how that happened, but that should be in a MM remake), all you would have to do is go back in time and prevent yourself from doing so.
Plus, as Flagpole suggested, it is a lot easier to save up rupees in the bank, go back in time, fill it up some more, go back in time, and it just goes on and on until you have 5000 rupees so that way you could get that heart piece. Plus, controlling time was interesting.
Now, the only problem I have ever encountered with the saving system is how it throws you immediately back into the game, which is exactly what it is supposed to do. I think of it as a downer because if you forgot what happened within the last time you played, you could be in a world of trouble. But, that is my only problem in my opinion. Other than that, I don't think there was something wrong with this. By the way, if you slow down time, you get at least two hours real time. Normal flow is just one hour real time.