Many seem to misunderstand on purpose and jump to conclusions before all the details are known. The last episode in TYT (ep. 18) when the magic disappeared for a short while to stop arguments between magically active ponies, obviously did not go down well with the fans - but MYM has shown how very dangerous the magic had become, and that this had to regulated as by holding back water with a dam. What is not realized about this is that this makes organized violence between ponies impossible, although it was clear that the Unity Crystals exaggerated where Sunny is forced to have mixed teams instead of pitting unicorns, earth ponies and pegasi against each other as we have seen many times in G4. It doesn’t leave a good taste in the fans’ mouths, to say the least. This is tolerated while waiting for this to be fixed. So far.
But this revealed that it is not the ponies that were the reason behind the disappearance of magic, when it can be easily turned off and like with a light switch. Discord stole the pegasus crystal, without the magic disappearing, and TYT ep. 18 shown that loss of magic is like slaps on the fingers by an angry teacher, to behave. Permanent loss of magic would be impossible under such circumstances. We’ve learned in the IDW comics that the Unity Crystals were forced on the Mane 6 who had never come out for such a disaster before, and that they can’t solve the problem then. We saw exactly why; MYM has shown that emotional energy comes from the ponies of the Unity Crystals, and there were many examples in G4 where this was important, such as when a village became colorless. All told, this was the Windigos’ fault, they had created an imbalance that got worse and worse with time, especially after Twilight destroyed them.
To make the magic neutral as it was before seems to be unattainable for Twilight - and for the human writers who are caught in a “catch 22” because of the G4 writers who thought coercion and threats were the right thing to do when raising children . There is a strong demand for this to be fixed, and it will only grow stronger with time. This is starting to dawn on the crew behind G5, who need to finish explaining how the Unity Crystals could have come about and can be justified in the face of the danger of unstable magic. When the movie ended, many believed that the magic went away because the ponies had turned against each other, which Sunny feared could be a coincidence when MYM was coming to an end. Twilight is blamed for this. But Discord and TYT ep. 18 has revealed that this is impossible, the magic will not disappear for good no matter what happens the Unity Crystals. It’s not just taking apart the crystals, and the ponies can’t attack each other without losing magic, which will return once it’s calmed down. Twilight had created an invulnerable object, which could not be split to take away the magic. Even for Discord who cannot destroy the Pegasus crystal.
Then only one last logical explanation remains; the magic disappeared through a deliberate and premeditated act by someone who was able to control the Unity Crystals and manipulate them. In the movie, it is clear that Sunny was chosen, not randomly picked among the ponies - and her alicorn powers indicate that she was given a special responsibility. In MYM, her cutie mark was glowing at certain times, and sometimes it looked like the Unity Crystals reacted to her, like when she got into an argument with Hitch. She was also the only one who could come out of the mysterious dimension along with a rainbow that contained the earth pony magic. It is possible that she can control the Unity Crystals - including shutting down the magic, permanently. Is this connected to the alicorn powers (we saw a spell book in the IDW comics with cutie marks of all the alicorns when Twilight created the crystals), or is this due to Twilight’s spell, which selected Sunny for an as yet unknown reason? Maybe because she is the element of Hope, but we don’t know this.
Either way, it means that Twilight was the one who removed the magic, by controlling the Unity Crystals, as an electrical engineer who can disable the entire “power plant” as the dam gives away “power” or magic to the ponies. Anyone who knew her from G4 knows that she does not have a personality that can lead to such extreme actions, even many centuries after the Mane 6 were dead, and she would not lack friends and acquaintances including “the immortals”, including Spike and Discord. She is the great heroine and a role model for Sunny who esteemed to restore the magic of friendship to the world, and cannot be eclipsed if G5 is to continue. She has the same role as the distant Celestia from the first seasons of G4 in today’s G5, whether she’s gone or not.
Then there is only one logical explanation; she was in a dire situation with no way out or possibility to save anyone without giving up something very essential. The ruins of Canterlot and the many hints indicate that Equestria - presumably the entire world - was attacked, by a power that used magic that will disappear if Twilight takes away all active magic. It may have cost Twilight a lot, as we know very little about the Unity Crystals - and why the Mane 6 are involved in this, even long after their time. Discord refused to explain or can’t, and his behavior in the IDW comics doesn’t indicate hostile intent - he was willing to sacrifice his own life as he ages when he doesn’t have magic as seen in Canterlot. The loss of one horn, his behavior and appearance suggest that he was exposed to traumatic experiences that caused him to reminisce about his time with his friends, specifically Fluttershy. Then that means it wasn’t just unstable magic that scares him.
What could have scared Twilight - one of the strongest magical beings in the Ponyverse - into taking such a drastic step and disappearing? In an IDW cover it was seen that she is fighting something unknown - and that things are not going well for her. In the end, she may have concluded that magic cannot be used, if her opponent is far stronger or more destructive with magic, and to save what can be saved - even if it will cause Equestria to collapse, which she knows all too well will happen, the magic must be gone. So she broke open the Unity Crystals - removing the magic permanently. She may have been in the most hopeless situation ever in her entire life, when everything else had failed.
We may get part of the answer at the beginning of the G5, but then Sunny must tackle challenges where Twilight had failed. And maybe she has to fight the mysterious enemy that even her role model couldn’t defeat. The lighthouse in Maretime Bay is lit, but the fire not only illuminates the world for a better time, it also attracts threats from near and far. It will be the Mane 5 (which may become the New Mane 6 in S2 or S3) who must guard the world.