Silly Druid

No, I don't mean Pony Life. Let's not talk about it, OK? I mean the events that caused the state of the world that we see at the beginning of the G5 movie, where the three pony tribes live separated from each other, and have a bad opinion of each other. If we try to reconstruct what happened, there are two important facts that we must take into account:

1. None of the races knew that the other ones didn't have magic, which means that the loss of magic must have happened after the separation.

2. The station in Zephyr Heights shows us that there was a period of "friendly separation", when the ponies lived in the same places where they live now, but there was friendship between them.

So here's what I think: First there must have been a war between the races. Maybe Tirek, Chrysalis and Cozy Glow managed to escape their stone prison and tried the same thing they did earlier. Or maybe it was some other villain, what's important is that the ponies were fighting against each other. The winners of this war are clearly the Pegasi, who captured Canterlot and renamed it to Zephyr Heights. This is not a surprise, because, since the times of Commander Hurricane and Flash Magnus, the Pegasi were highly militaristic, so the warrior spirit is probably still strong within them. The losers were the Unicorns, which is surprising because they had powerful magic. Maybe Pegasi and Earth Ponies teamed up against them? Anyway, the result was that they had to retreat to the forest, and make it their new home.

After that, the villain's schemes were uncovered, and the friendship between the pony races returned. But the separation already happened during the war, so they continued to live in their own parts of the world. This is probably the time when the Three Crystals were created, and when the station in Zephyr Heights was built. What happened next is probably just politics. In all of the three tribes, the ones who rose to power were using populist propaganda to achieve their goals, which resulted in the loss of trust and communication between the races, and, as a result, the magic was gone too. Because, you know, friendship is magic, so no friendship means no magic. But why didn't the magic disappear during the earlier war? Well, maybe the process takes some time, and the war was probably pretty short. But it is possible that it was getting weaker during the war, which is another explanation of the Unicorns getting defeated.