Background Pony #84E8
In my headcanon the Unity Crystals have a mind of their own. They can punish ponies or any other creature that threat harmony.
It was because the magic was unstable; the “dam” didn’t work properly - and this episode proved that all ponies actually have magic, even if their “foci” are moved to the Unity Crystals. It explains why ponies have cutie marks which we know are based on the talent magic, and they only have one instead of both flanks. They generate internal magic, but likely cannot channel it for manipulation without the assistance of the “magic pool” in the mystical dimension. This cannot be erased in a world with a magically inactive background that allowed the existence of magical creatures and basic magic.
The earth ponies didn’t get magic and we don’t yet have an answer, but maybe the hypothesis that the Unity Crystals can be manipulated and then controlled by the “chosen” can be used here. It was only after Sunny became an alicorn that the crystals assembled, possibly after being “commanded” to release the magic. But the process was not complete, a dam has floodgates to release water under control, and that may be how the magic is released through the Unity Crystals. So what Twilight may have done was to close those gates so the magic didn’t get out. Then it meant that all gates were not open at the same time.
TYT ep.18 showed what the earth ponies’ dissatisfaction would have led to if they had magic, but in MYM they only had the internal magic - which unfortunately releases emotional backlash to the Unity Crystals where the Earth Pony crystal almost burst. Some of what had happened before the Unity Crystals were created had perhaps arisen because Sunny did not know what needed to be done. It was only after she tore out the earth pony magic from the mysterious dimension that the magic stabilized, where the Unity Crystals once again functioned properly.
Perhaps the Unity Crystals were not unique, and perhaps have many floodgates for different magic meant for the entire world. But what happened when the magic disappeared was probably a total shutdown. Can only hope that Sunny has opened all the gates if this hypothesis is correct. I can think the other non-ponies also have their own Unity Crystals, but that they may have also been shut down because of Twilight.
But then it also means that if the Unity Crystals can be controlled, possibly only by those with alicorn powers, it is perhaps not so strange that Shadowy will take the pony magic for her own plans which involve creating a “perfect” Equestria. She wants to be able to decide who can and can’t have magic. She was prevented for three reasons; firstly that the Unity Crystals probably denied her, secondly the unstable magic that she couldn’t handle, and thirdly the disappearance of the magic. Twilight protected the Unity Crystals from potential tyrants like Shadowy - until a much bigger threat arrived.
Then the title “defenders of the Unity Crystals” is serious. Until the Mane 5 or others manage to make the magic immune to emotional influence so it can become completely neutral. But then someone has to dive deep into the ponies’ mysterious and dark past, and have someone on the “inside” of the dam which is a kind of “door” to the mysterious dimension from which the magic came. Maybe that’s where Twilight or Mane 6 could show up in G5.
So I wouldn’t rule out the possibility of an intelligence behind the Unity Crystals as seen when Sunny was chosen as “their” alicorn.