The Shadow Triad somehow has access to the timespace orbs with no explanation as to how they got them. They just hand them to the player.
Cynthia allegedly skinny-dips near her villa in Undella town when no one is looking.
Cynthia is interested in the myths of Sinnoh.
Cynthia doesn't do jack shit in the Distortion World despite being Champion, even though she could've easily defeated Cyrus herself (compare with Lance, who helps you in the Team Rocket hideout in Mahogany or Steven, who helps you in the Mosdeep Space Center). Only the three Lake Guardians help you.
We now know that her ancestor Volo is a schizo with a god complex.
Doesn't it check out?