Honestly I think that they wanted to do something similar to Allison's twin from the books, and assumed that the sister in this case being transgender and telling us all to look out for a male character called Charles would be a shocking enough twist to impress everyone with the A reveal, but one big twist just isn't enough when you've spend nearly 4 seasons building up to that mystery. I think that they were banking a lot on Charles really being a female character being enough to induce huge gasps and get talked about as being something that nobody saw coming. But then the episode just felt like such an exposition dump with the writers straining to reach for emotional pathos. I mean I've brought it up a couple of times now lol, but it was a big let-down to give us no interesting motive for CeCe targeting the main characters. It seemed like they should have been incidental in her goal to establish a connection with Allison and Jason, yet she spend way more time on her sisters friends for some reason, apparently she didn't even know that Allison was still alive until the season 3 finale!

To defend the show for a moment though, wasn't it Mona who was the original A from the Halloween flashback, sending the notes on it being my turn to torture you? As far as I'm aware A was just supposed to be Mona for the first two seasons, hence the irony in Mona convincing Allison to run away for protection when she was A all along. They only introduced the new A mystery in season 3, they just made it seem in the season 2 finale that there was an uber A that Mona was taking orders from. That was another slightly disappointing reveal though to just hand wave it as oh Mona was really drugged up at the time and didn't know what she was saying , although I suppose it was a good twist that makes sense in retrospect that she believed that she was really talking to Allison when it was actually CeCe.