It's not even that, really; in this new verse, she was never roboticized. Instead she was injured during Eggman's initial attack, and her limbs were given to her by Uncle Chuck as a means of saving her life.
Uncle Ben DOES NOT Approve
Of course you don't. In fact, you've been saying that a lot lately. I don't get what's so wrong with this...
She was never roboticized. Thats whats wrong with it.
So what? Instead of getting half way roboticized, she gets her robotics from injuries from Robotnik's first attack. That's way more interesting than having her go into a roboticizer, turn herself half robot, and then BOOM, Freedom Fighter.
Largely because it nullifies the more powerful subtext of her own personal arc; escaping enslavement at the hands of a very terrible enemy and being marked for it, chasing the hope of returning to a normal life and then learning that ultimately she can never go back.
While the incident itself was presented during the more humorous days, the characterization took that turn as things went on, and it was one of the more striking aspects of Bunnie's character, along with her fears of what it might do to her, fears which were realized when she learned that her limbs were poisoning her.
For her to simply be collateral damage, rather than the only one to escape Roboticization, ultimately takes away from the personal nature of what happened to her, as well as taking away that reminder of what the Freedom Fighters face if they should lose. Her condition the last time around was the result of her being deliberately targeted; here, she is just collateral damage, and there is really nothing particularly unique to this new backstory.
It's somewhat underwhelming, and furthermore it also takes away from Eggman's own villainy that this happened without him intending it. While definitely callous, it doesn't really stand out in any way, and diminishes the personal nature of the conflict.