One of the twins choking (and then biting) Annabella definitely makes sense. For one, having two bullies who tag team against her makes it more likely that Annabella would point the finger elsewhere. More importantly, though, it adds meaning to Perry abusing Celeste, since it means that they picked it up from him. It'd make the most sense if one secretly saw Perry choke Celeste and then acted that out on Annabella, but, even without that, you can see the influence of Perry's aggressive tendencies in how the twins run around firing toy guns, even at innocent people like Celeste. It's also interesting how Perry often pretends to be a "monster" around his kids when he's really a monster in real life (to Celeste and, possibly, to Jane, if he was her assaulter).
There's also interesting potential for a contrast between the twins and Ziggy if Perry is Ziggy's dad and one of the twins is bullying Annabella. All three boys would then be Perry's biological children, but the two that he fathers are the little monsters while the one that he's never seen is the little angel. It would highlight how you're not a bad person because of nature, but because of nurturing.
If all of that is true, it makes sense that Perry is going to have a huge meltdown in the final episode. He'll be faced with losing his marriage, losing custody of his kids and potentially being charged with rape (or, at least, losing his reputation because of the accusation). I suspect that he'll flip out, get super aggressive and end up being shot. Celeste and Jane would have the most reason to shoot him, but that's why they're probably not the shooters. It'll likely be committed with Jane's gun, since that's the prime weapon highlighted in the series (and part of detective work, which the series is told through, is tracing the murder weapon), but I'm guessing that it'll be by Madeline, who is closest to Jane and has the best access to the gun. Madeline is also shown nearly every episode driving by the bluffs where I think that we're led to believe that the shooting takes place.
So, my best guess is that Madeline shoots Perry because he threatens/attacks Celeste and/or Jane, who just happen to be Madeline's two best friends. Perry getting shot wouldn't be shocking, but Madeline doing the shooting would be, and it would also make dramatic sense for probably the show's biggest star and America's sweetheart to be the shooter. It would likely be a justifiable shooting that she'd get away with, of course, since it wouldn't at all be a satisfying ending if a very likable star and mom of a young child on the show were to go to prison. America's sweetheart giving to an odious person exactly what he's deserved all season and getting away with it because it was deemed to be justified sounds like a way for the series to have a very satisfying conclusion.
Anyways, that's my best guess for what happens. Who knows, though. My theory doesn't take into account Nathan, his new wife, Nathan and Madeline's teenage daughter, Ed or the guy who Madeline cheated with. How do they fit into the murder or are they red herrings? It would certainly be really impressive and satisfying if every single character and story thread fit in somehow, but it's impossible to imagine how.