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.
On a similar note, do you suppose the others — including Shining Armor, who was brainwashed at the time — ever forgave themselves?
Let's say that even if they managed to get the Elements on time but only to fail. Twilight may not hold grudges but the elements failing to work because the other Mane Five going against their elements.
The Queen's name is Chrysalis. After she beats Celestia and the Princess loses consciousness — where does she wake up? In a chrysalis. Does this mean that the Changelings spin chrysalises around other ponies and change them into creatures like themselves?
Queen Chrysalis seemed to be goading Twilight into using her magic down in the caves. She did this knowing that it might uncover the real Cadance. She could have been hoping that Twilight would kill the real Cadance with her magic. And given how furious Twilight was at the time, she probably would have if Cadance hadn't remembered the Secret Handshake to prove she was the real one.