These days I believe Nicole wouldn't have been left only as a gadget - she'd definitely get a visualized virtual model, lynx or otherwise. Not that it makes much sense in terms of being easier to use or provide more functionality, but everything has to have a face and personality now. She'd probably get an advanced A.I. to make insightful observations and provide some fun and/or embarassing moments. If she's portrayed more logical, then she'd comment on Sally's course of actions being swayed by her affection to Sonic rather than logic. Or she could be given a distinct personality to say the same things as a friendly joke.
The robotization process would probably be the most polarizing question. In the 90s it was just a small plotpoint - a mad scientist turns animals into robots, but you can undo it via destroying the metal body and releasing the host (the games) or by some unspecified incomplete transformation device (SatAM). Nowadays it'd get much more attention. How could a machine turn living tissue into a machine? Some Robocop NSFW imagery ensues. Even still, how can one derobotize someone back to their previous self? Nightmare fuel. There could be superscience at work, with machines rebuilding living tissue as needed, but then the whole technology in the series should be portrayed as extremely advanced, which may not be suitable for the premise of the series. The alternative is even worse - if the robotization process in irreversible, then the plot might look too grim to be a cartoon for more or less wide audience. Then again, there's Bunnie. It has to be explained to some extent how her body works. Metal feet have to hold on to organic parts somehow. Wouldn't they be too heavy without the whole exoskeleton? Does she need to charge them somehow? Does she need to eat more to fuel them up? It's hard to pass up such questions nowadays.