No wants to remember her but we have to. She is considered one of the most hated characters in the Sonic franchise for many reasons. The comics are obligated to add her to the series she would take effect later on. This means we have remake her profile.

We faced the fact before in Sonic Generations as they reminded of 06 although was not that bad.

As they are free to change aspect from the source they allowed to make alter or retcon it nothing new my guess the would use Ixis magic to explain why everyone was out of character. I believe she would do it or the evil Ixis wizards like Ixis Naugus or Mammoth Mongul. Mamoth Mogul said he was betrayed in the future. so there is one clue but he is being senial. As you Mephelis is in the zone cop jail so he could have made some effect before he was arrested so there is there second plot device.