It has been brought up that while Twilight had been right all along, she handled it in an immature way that caused everyone to turn on her. Trouble is, suppose she had handled the situation calmly and maturely? She would bring her concerns to Celestia, who might decide to test her student's theory, if only to give her peace of mind. She'd get Fake!Cadence alone and strike up a conversation with her, maybe discuss an event with details only the real Cadence would know. When Fake!Cadence slips up and reveals herself, she may indeed not yet be strong enough to take Celestia in a magical duel. Chrysalis is captured, yes, and her Evil Plan foiled, but what about Real!Cadence? Only Chrysalis knows where she is and do you think she'll be eager to tell?
Either that or it'd take an elaborate search party to help locate the real Cadance, especially while there may be some ponies who actually do remember the caves beneath Canterlot despite Chrysalis' insistence that they are long forgotten.
What if Twilight was wrong? The series would involve Twilight atoning her mistakes and (as shown in Lesson Zero) she can be scary hard on herself. Even if Cadence and everyone else eventually forgave her, she wouldn't forgive herself.