>>36833460Okay, lets put our pony thinky caps on and play. First, I think your estimation of the Equestrian population is too high. There are only about 2 dozen pony settlements listed across the multitude of media for FiM. These locations very in size between the well established Canterlot to the newly founded Applelossa. I've seen other threads attempting to count the pony population and I'm not going to bring them out here because it's all speculation, but I do think an estimation of a quarter billion is too high. That said, I do agree with the point you were making that the population seems to have decreased since FiM.
Make Your Mark Episode 6 does give us some information about the start of the downslide. Apparently during Twilight's reign, an Earth pony was hurt by a Unicorn and this led to mass disagreements. (an interesting note at this point is it is never stated a Unicorn physically or intentionally hurt an Earth pony and the image that accompanies these lines are a cracking heart, perhaps suggesting an emotional discourse.) Twilight striped the population of magic to keep things from getting out of control and placed the magic in three crystals, giving each one to a different tribe. That way, ponies wouldn't have magic until they learned to come together again. Misty offers a second explanation says Twilight took the magic away to keep it from Ovaltine, then sealed the pony lands in a magical bubble to keep Ovaltine from finding the crystals. The bubble part is likely true as it explains why Ovaltine keeps Misty around and Misty would have first hand knowledge of the bubble if she lives outside of it with Ovaltine and needs to cross it every time she sneaks into Maretime Bay. The truth is likely a mix of both stories, with Ovaltine either causing or being one of the involved parties in the discourse. Twilight's message mentioned Ovaltine's attempt to take all magic for herself and it makes more sense for a motivation for what Twilight did than what Sunny offers.
So unfortuately, it looks like your magical pony war was prevented by Twilight Sparkle. To keep such a thing from happening, she striped all ponies of their magic. Unicorns could no longer do horn things and Pegasuseseses couldn't fly or control the weather. They maybe had a physical battle, but neither of our G5 historians made reference to one. Battles in Equestria are typically fought physically anyways, as we can see when Starlight Glimmer causes the war with Sombra in another timeline. You would think it would be part of at least Sunny's story if it occurred, rather than just referencing one event of Unicorn on Earth pony violence.
So what could have contributed to the decline? Maybe Windegos? That's what came in the Hearthswarming tale. I kind of think the magic bubble keeps out magical races though. It explains the absence of Dragons and Griffins and Kirins and all the other fun magic races. Sparky got through because he's an egg. This however has a problem in that Ovaltine in very excited by the possibly of Dragonfire. If she was trapped outside the bubble, and so were the dragons, she could get dragonfire far more easily if she went after the dragons outside, where her powers still work (whatever those powers are). Maybe it's Ovaltine who's actually inside the bubble, not Equestria.
One more piece to the puzzle that doesn't fit yet is Earth Pony magic. Twilight knew it was coming, because she references it in her message, but she also says it's been activated for the first time ever. So Twilight's actions with the crystals therefore either created or prevented Earth Pony magic. It could be a result of the crystals spreading magic to all races, or perhaps it is a natural evolution of magic, which Twilight says is always growing and changing.
Another fun thing to think about is the Cakes. Their family isn't all the same tribal race. Were they split apart by these events? We also know from them that the tribe of a foal doesn't always match the tribe of the parents. So for the first few generations, was the occasional child exiled for not being born the same tribe? There's a fun fanfic for someone to write.
My TL:DR, nope, I don't think there was a big race war because I don't find any supporting facts, but I admit it would be cool. I don't yet know a reason for the decline in population, but I am filing away clues as I find them. Maybe they all went to live with Sunset Shimmer to avoid the magic stealing tyranny of Twilight Sparkle.