My humble contribution to making Amy suffer is to let her spend more time with Bonesaw.
Imagine, if you will, Amy stuck with Bonesaw (as her handler), just like in Ward. Now, whether this does happen post-Wretch or not is irrelevant, but I do believe it's funnier if it does.
Amy has to take care of Bonesaw. She has to double-check her work (and, more insultingly, the reverse is also true). Amy is also kind of stuck, because while Bonesaw can do things Amy herself can't ("Oh, of course I can make you non-permanent prosthetic arms, I can be trusted within 15.98 feet of other parahumans really", "Fix your brain and power after a bad trigger? Lemme take a peek!" "Yes, I can make a case 53 human again! And I can make it ("her", says Amy) - I mean her- the most beautiful artwork ever!")
So Amy is stuck with this little, annoying, traumatized tyke with blond hair and blue eyes, and for the first time in her life she's both the Responsible One and the Not That Evil In Comparison one. She still heals people on the side, but a significant portion of her day is spent around Riley, who can turn a man into a toaster in less than twelve minutes but the last time they asked her to actually make food she somehow whipped up bile that tastes like strawberry ice cream to the hatred of everyone involved, so now they all look at Amy expectantly since she's the only one who's not scared of the girl whose small size is inversely proportional to her body count.
So Amy has to teach her what a balanced breakfast looks like and how to make it instead of "Oh I just extract the fat from my body surgically once a week" and how to have some bedside manners instead of saying "Hello, what totally ethical, totally non-invasive surgery with no bad consequences can I perform on you today?" and how to pet a dog instead of asking if she can turn it into spare organs (what the hell Riley, Amy only did it once).
More and more shit is put on Amy's plate since the PRT doesn't believe in child slavery or criminal slavery and thus Riley is treated like a young cape and thus should get an education like one, and who's the only person they can trust around Bonesaw, the one gal who's not going to wake up at the end of the study session convinced it all went well with suspicious scars at the back of her skull and Riley whistling with a bloody circular saw behind her back? Panacea. What's that, it's cutting into healing-people time? Well, it's not like people really trust The Wretcher, so it's all for the best really. By the way, Bonesaw is making prosthetic hands for Damsel of Distress, can you look after them? So Amy has to spend time sitting at a desk next to a little girl who is perfectly aware of Amy's bullshit and teaching her math and history, as if she had nothing better to do.
("Oh wow, look Amy, this Cleopatra girl almost married her brother! Isn't that romantic?" "I will bloat your tongue with so much cancer you'll never speak again." "I can replace it with a speaker!")
A lot of time goes by, Bonesaw grows up with Amy acting as the best, grumpiest big sister in the world. And at the same time, Amy kind of comes to see Riley as an annoying little sister too, in a weird way. They bond over healing, she teaches her things, and Amy feels almost proud each time Riley really heals someone without bad surprises (and yes, reinforcing someone's muscles with titanium mesh without their consent is a bad surprise, stop it. No, removing a potential cancer isn't the same thing, shut up.)
Then one day Amy turns around and sees teenage Riley looking at her with googly eyes, and Riley blushes a little when they touch, and is she is looking for excuses to spend even more time around Amy?
She realizes with dread that Riley has a crush on her. A crush that is painfully obvious. A crush that could not be more awkward because eww.
For the first time of her life, Amy is fully, totally in Victoria's shoes and she hates it.