Okay my theory is:
Charles and Jason are the Di Laurentis twins, fathered by Peter Hastings, as seen in the video, also seen is a baby girl, not Alison, another daughter. After concieving the twins Mrs D moved her family away in a bid to cover up the real paternity of her kids. Whilst living away Charles kills the young baby accidentally and the family send him to Radley and try to pretend it never happened, taking away all pictures, moving back to Rosewood and having Alison. Alison becomes the number one child because she reminds them of what they lost, whereas Jason who reminds them of his murderous twin is pushed aside. Charles visits home once but breaks Alisons arm and never returns again.
Flashing forward, Mrs D brought two yellow dresses, one for Ally and one for the girl she had lost, but she asks Ali to keep it quiet.
Flash forward again and Mrs D whilst visiting Radley discovers Charles has a girlfriend, Bethany Young and so, seeing it as a chance to replace her missing daughter, lavishes the girl, meanwhile Bethany is tortured inside drawing hateful art as a reflection of what Charles is telling her about his evil family.
One night Charles and Bethany break out (the phone call Mrs D receives was a warning), wanting to confront Mrs D, Charles sees Alison, hits her over the head and Mrs D wanting to cover it up, buries her, Grunwald saves her. Jessica the other missing girl (remember her? They met her friends?) is Alisons friend and comes to visit her, Charles and Bethany having returned to the scene, is enraged to see what he thinks is Alison again, alive, and hits her again. Melissa buries her thinking its Alison and Spencer did it. (Melissa being the one who actually killed Jessica because didnt the report say she was alive when buried?)
Charles is returned back to Radley with nobody knowing any different. At some point in his lifetime at Radley, he meets Tobys mom and cares for her before she kills herself.
Bethany Young goes on the run.
(I know they identified the body as Bethany but hell, they though it was Alison at one point!)
Meanwhile Mona assumes the identity of A, is caught, locked up, and meets Charles, who takes over the game and forces Mona to work for him, without her ever knowing. Red coat is Bethany, working for Charles. At some point Charles is released again and at this point, interactions with Jason and everyone else could sometimes have been Charles? Things like, when he kissed Aria and was taking all those creepy ass photos, that was Charles, not Jason. Charles eventually wants to end Jason and assume his identity (like dropping Jason in the lift?)
At some point Charles stops hating Alison and realizes she is his one link to a real family, she could replace his sister and make everything okay so his end game is getting her (hes tried many times, in NY, in hr house etc) the liars are a big part of getting Alison, he knows she would want her friends so he plots to take them aswell, so she can be happy. But Mona double crosses him and Charles decides to take her instead, making her his Alison and leaving the real one to rot/maybe eventually killing her.
He killed Mrs D. He either killed Maya (and Nate took the bullet.. literally) or he has her too because she figured it out after finding things in the house when she moved in. He knew Garrett and Ian etc because he was following Jasons life also. He went after Jasons friends because he saw Jasons life as the one he should of had.
Charles knows Spencer is also his sister, its why he saved her from Ian, (That wasnt Mona)
Marlene said Charles is someone we've seen since season one. So hes either Jason and Jason is playing both parts of his twin, or its someone else (which would blow a hole in my whole Charles pretending to be Jason thing) that we've seen often, like Wren, Andrew etc.
Phewwww, thats my theory. Although i have read someone say that Toby is the other twin and he doesnt know and Jason is Charles.