>>44786560Cynthia gains her wheelchair by being injured by Dialga / Palkia / Giratina, putting herself in harm's way to protect her Pokemon. As a younger trainer she was obsessed with the legends of the region, going so far as to track down the deities, but she had to seal them away when they turned out to be angry, violent and too powerful for her.
(This is important as it gives Cynthia a valid reason to be so familiar with the legends and particularly the Distortion World. It also shows Legendary Pokémon as actually threatening and powerful, something not usually shown so explicitly in-game.
Cynthia now uses everything in her power to stop people pursuing the legends, both out of fear and respect to them, and to protect humans from being injured or killed. Her strength as a trainer comes from her desire to keep the people of the region safe: becoming champion was not her goal but something that happened along the way.
There has never been a visibly disabled character in a Pokemon game, despite many disabled kids being fans of the series. I think it would be brave to make the first wheelchair user in the games the strongest trainer of all. (Additionally, Cynthia should be proud of her chair as she considers it the changing point in her life, so that she can be a positive role model and not a tragic character. TPC could even donate wheelchairs in the design of Cynthia's chair to children's hospitals in a promotional act of charity.)