If you haven't read the Pretty Little Liars books and don't want to hear any theories that may contain spoilers you should probably turn back now. If you read the Pretty Little Liars novels, you know that the twin storyline was originally with Ali, and her twin sister, Courtney. Similar to the way in which Mary Drake has now shown up in the show now that Mrs. D is dead, Courtney showed up in the books after Ali's body was found. There's a lot of similarities between the twin storyline in the books and the show, but one main plot point people have been wondering about is if Mary Drake is actually Mrs. DiLaurentis.
In the books, one of the greatest plot twists was that Courtney was actually Alison. Just as Mary Drake was sent to Radley, Courtney was sent to a psychiatric hospital when she and Ali were younger. On one family visit home, Courtney switched necklaces with Ali (her's was a 'C' and Ali's was an 'A') and befriended Hanna, Spencer, Emily, and Aria to help corroborate her story that she was in fact Ali and not Courtney. Although Ali tried to make her parents believe that she was the real Ali they didn't believe her, thinking it was Courtney just being unstable and projecting onto her sister. So, Ali was put into the hospital and Courtney got to live as Ali.
That is until Ali came back for another family visit and killed Courtney. She then plotted revenge against the Liars because she blamed them for being the reason why Courtney was able to steal her life. Later Ali gets out of the hospital and comes back to Rosewood as Courtney, Ali's long lost twin sister, and befriends the Liars while actually plotting against them the whole time. Did you follow that?
If the Pretty Little Liars writers are really transferring the Alison twin plot line to Mrs. DiLaurentis and Mary Drake, then it would make sense that this is exactly what has happened. At some point, Mary Drake might have been able to switch places with Mrs. DiLaurentis, living her life and pretending to be her. The real Mrs. DiLaurentis then got out of Radley and killed Mary Drake for stealing her life, and that's who really killed "Mrs. DiLaurentis." Now the real Mrs. D is back as Mary Drake.
There's just one major issue with this theory: Charlotte. If Mary Drake is actually Mrs. D, why would she care about avenging Charlotte? Unless Charlotte is actually Mrs. D's daughter as it was originally believed. But then does that mean Ali and Jason are actually Mary Drake's children? This is all very confusing.
It'd be interesting if Mary Drake is in fact Mrs. D, but in this context it just might not make much sense. Then again, when it comes to the DiLaurentis family, nothing ever does.