Perhaps blasphemously, I found that I enjoyed Sonic Underground more.
Yup, that's blasphemy, alright. Everyone get your torches ready!
Naw, seriously, I can't be objective about this. And it's been YEARS since I've seen Underground, so I barely remember most of it. It's..."possible"...that Underground is the more fun show. I guess. *grumble*
What really interested me is what it made me think of and it seemed like the comic writers post "throw Ken Penders characters into a portal" wave were also thinking in that her origin was changed from incomplete roboticization to (sci fi) prosthetics from surviving an Eggman attack. It's a parallel not really shared by others in the mainline franchise.
There's actually a long story about that. (A long story...about the Archie comic?....I know I'm surprised, too.)
In Sonic Super Special 11 (October 1999) Bunnie's roboticized limbs started to malfunction. She has a choice about either replacing her roboticized limbs with purely robotic ones (which can NEVER be de-roboticized) or attempt de-roboticization at the risk of her life. She chooses to replace her original limbs with robotic ones, so she can continue the fight. This was probably to give Bunnie some agency and control over her own destiny. And a excuse for a re-design.
In Sonic the Hedgehog 129 (October 2003), a alien race called the Bem have a contest to see which is superior, robotic or organic lifeforms. This leads to the de-roboticization of all the Robians on Mobius. And roboticization is actually rendered impossible from then onward due to a special energy field. Which was a way to get Eggman/Robotnik to create more classic robots like in the games. Bunnie remains the same due to her artificial limbs.
Later in Sonic the Hedgehog 232 (December 2011), Ixis Naugus used his magic on Bunnie and accidentally magically restored her organic limbs, while trying to prove he deserved to be the new king of the Mobians.
Eventually, Antoine, her-then husband, was put into a coma. And in Sonic Universe 48 (January 2013) Bunnie went on a journey to get her robotic limbs BACK again, to be more useful in fights, from some former Dark Legion members lead by her uncle(Knuckles' enemies from his comic).
Then the Super Genesis Wave happened and reset continuity. In this version of events, Bunnie is injured by Robotnik's attack and Uncle Chuck used a experimental roboticizer to save her life. It's not Robotnik's roboticizer anymore, but she still had to replace her roboticized limbs with artificial ones, even in this new continuity. This is revealed in Sonic the Hedgehog 255 (December 2013) and GREATLY expanded upon in "Sonic Comic Origins-The Belle in the Machine" from Sonic Super Digest Special 9 (October 2014), and this is where she actually has to train up her body to use the artificial limbs. And that remained the status quo until Archie lost the license.
Simple, right?