the Doom Patrol's powers/problems directly reflect their flaws before their accidents.
Larry couldn't ever humor living a life with John, out and proud. He could never leave his wife or even tell her he was gay, so much so he hurt John.
Larry now has to cover himself in bandages and hide himself away—not just because of his ugly burns but because he's radioactive. He literally can't be open with himself and who he is.
Rita was close minded, specifically towards an amputee. Specifically calling the man an eyesore and a liability.
What now? Rita finds herself entirely ugly and can't bare to look at herself in fear she'll fall apart. She's permanently disfigured in a way she can only mask and hide. When the crew hit the town she's the one who gives them a bad name and blows everything up—now she's the liability.
Cliff was all about living in the moment, the thrills the taboo. He cheated and he raced cars for a living.
And yet it wasn't racing on the track that killed him. He didn't go out in glory and came and heartbreak, but because of one of his mistakes. Mistakes over and over again, how many need to stack up until you're just a horrible person? He's all about fucking and yet loses his body entirely. He's selfish and for once it blows back up into his face.
Victor makes rash decisions in the heat of the moment, it got his mom killed.
Now he has to deal with hypersensitive uneasy AI and getting it under control, so much so he ends up getting rid of it to be normal again.
And, well I have nothing to say about Jane. She's the one who's the least self flawed since the beginning i suppose, besides her rudeness but they're all pretty rude in the beginning. Victor is a more light example of this phenomenon too.
Anyways—through the course of the series they grow to control their powers, and by proxy outgrow their flaws.
Larry finds love in someone who isn't harmed by his radiation.
Rita learns to love herself, and others, and by doing so learns to control her powers.
And Cliff, when Cliff gets his sense of touch, he doesn't waste it or be greedy with it. He saves it for almost like a whole season to finally do what's right—put his family, his grandson, first.
And they do all of this without Niles. They outshed the harmful confines of the powers he gave them and learn to become their better selves while doing so. He wanted to help them after hurting them? Well he doesn't get the chance to, and that's the greatest protest they could ever give to his spirit:
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