To be fair a few of them are pretty easy to miss. Getting Mewtwo in WLL requires the true ending, Diancie is only mentioned in a sidequest, Isha only uses Giratina if Lavender doesn't release it, and Stakataka is only mentioned in V13. As for the school of nightmares, I'm pretty sure the Unova dragons were part of a deal with the Puppet Master, but with how much money and influence the Blakeorys have it seems pretty reasonable that they would be able to get a Genesect