I have 2 Quantico theories (that probably aren't unique)
Theory 1 (and probably the most common out of the two): Booth did it. He’s the only one who’s been close to Parrish since the beginning. He could’ve easily either gotten someone to shoot him or shot himself. The excuse of him being recruited to spy on her made it easy for him to do everything. AND he’s one of the two people who was written off IMMEDIATELY to doing it. (someone wrote a great analysis of why Booth might be guily that I completely agree with so if you wanna read it, its here.)
The other person who was written off IMMEDIATELY?
Theory 2: Alex ACTUALLY did it. You assume that she didn’t do it because from the get go, (i.e. before the show even premiered, through promos and such) it was claimed that she was framed. That automatically bring your focus to everyone else. The ENTIRE show has been around her trying to figure out who framed her, but you have to take into consideration that this is a show about the FBI. It’s going to involve a HUGE twist in some way. Also, they are literally TRAINED how to be FBI agents and, by default, how they think. She knows how the FBI thinks and operates. That way she’s always a few steps ahead, which mirrors how she does in her training. She’s at the top of her class, so she knows and can do a lot, AND, more importantly, she’s usually thinking a few steps ahead of everyone else.
Also, I don’t know a lot about TV, but I know enough to know that Alex actually doing it would be the only way of getting a good enough reaction from the audience, especially since pretty much everyone else is made out to be suspicious.
I just thought of another theory while writing this of her mom doing it, but I don’t know…its possible but it’d be completely left field.
EDIT: I now have another theory of Alex and Booth working together.