So they were created by the Titans, right? Constructs of Terracotta and whatnot. Well, if that is true, then why was the last Emperor of Pandaria a Pandaren?
Well here is what I figured out.
Y'Shaarj was killed over Pandaria some X amount of thousands of years ago. How long, we don't really know. But what we do know is that there were plenty of Mogu constructs that fought the Old Gods and their Minions alongside the other Titan creations. Well, in addition to Y'Shaarj dropping the Seven Sha around Pandaria, I think he also perpetuated the Curse of Flesh early in the region.
This would explain why the Mogu would have been creatures of flesh long before the Sundering which was 10,000 years prior to WoW, and during the Sundering Shaohao, a Pandaren, was the Emperor of Pandaria.
This would lead to another question, why wouldn't the Night Elves remember the Mogu, because they remember the Pandaren to some extent.
Well, I figure that during the Mogu Dynasties, there were no Night Elves. According to WoWpedia, Night elves really didn't start popping up until 16,000 years prior to WoW. This would give the multiple Dynasties of Pandaria ample time to have all of the many Mogu Emperors, up to Lei Shen, as well as the Jinyu, Hozen, and Pandaren Emperors, with the last being Shaohao.
And then to wrap up the 'Night Elf thing', it would explain the Zandalari Alliance with the Mogu. If there were only Trolls and Tauren in the world outside of Pandaria at the time, then it would make sense if the trolls did meet the Mogu, which according to the Zandalari Incursions in Kun-lai as well as with 5.2, they do have a racial memory and cultural memory of the Mogu.
Anyway, got that off my chest, what do the rest of you think about this?