First, I want to say I love this. There's so many threads that can tie together on the show it feels like a wasted opportunity.
So my top three or four ideas/theories I wish had played out:
Adoption/family seemed like such a big theme within the show, I always suspected one of the Liars were adopted or had some hidden secret sibling. Not a Charlotte or Sara, but someone interesting.
The N.A.T Club was the origin of Uber A. That the "someone else" Jason and the others were filming for was the unofficial fourth member and this was how they got their start, stockpiling secrets and cash, and then this person decided they wanted to do more on their own. And this person also started targeting the other members so it never came out.
That Alison planned to fake her death and did, but something went wrong. That Uber A was actually smart and figured it out (or even manipulated her into it) so it would be easier to grab her, because no one was looking for Alison. I would have liked if she spent those lost years when she was missing either kidnapped by Uber A, waiting for the Dollhouse to be finished to move her there, and she managed to get out at some point or she faked her way into a mental institution to hide out somewhere else, not Radley.
I would have either Ezra and Wren or Ezra and Aria to be Uber A. I would like it to be a strangers on a train scenario where Ezra and Wren met and each some agenda with the Liars and decided to help each other out. For Aria and Ezra, I thought in the middle seasons they did a good job of showing how they could be A together with minimal plot holes (Ezra is rich, and an adult so he took care of that; Aria had her share of shady clues and always seemed to know more than she let on/foreshadowed things A knew, etc.)
I would also have had Bethany Young play a bigger role in the story, had her be Alison's twin that was adopted or simply Alison viewed her as competition and lured her there that night when she found out her mother had an affair in Radley. She would be the girl in the grave, and Alison would have struck a deal with Mona or even did it by herself, to trick Bethany into being hit that night and mistaken for her. In exchange, she left Rosewood for good to Mona who agreed to leave her alone. But someone else was watching that night and found out, which is why Alison and Mona would both be targets.
Bethany would possibly be important to Wren or Ezra, the sister they grew up with that was troubled, and I like the theory the Liars had their own plan to kill Ali that night or maybe it just snowballed, and Aria was the one that hit Bethany to protect Spencer, thinking it was Ali. So Bethany would be the key motivating factor, or at least a big one.
I also liked the idea there was some creepy obsession between Ali/Aria and they liked to "trade personalities" with each other but Aria took it too far by becoming A, or it just was a toxic relationship all around.