If Cinder was Ruby in fanfiction, the RWBY world would be in for a shock. Ruby has a certain innocence and purity about her that Cinder lacks. Cinder being in Ruby's place would mean that her actions would be guided by her own self - serving motives rather than Ruby's selfless ones. The story could show how the other characters slowly realize that something is off about 'Ruby'. They might start to suspect that she's not the same person they once knew. This would lead to a breakdown in relationships and alliances. And in the grand scheme of things, the fight against Salem would be affected as well, as Cinder - as Ruby - could potentially make deals with Salem that the real Ruby never would.
It would be a whole new story. Ruby is often seen as the underdog trying to prove herself and do good. Cinder, as Ruby, would likely turn that on its head. She might take advantage of Ruby's relationships with the other characters, like her sister Yang. Maybe she would try to use Yang's protectiveness of Ruby to her advantage. And in terms of the fight against Salem, Cinder - as Ruby - could have a very different strategy. Instead of the more straightforward good - vs - evil approach that Ruby might take, Cinder could try to play both sides for her own gain.