Ani - I was willing to give the actress the benefit of the doubt in the first few episodes because the insertion of a brand new character into the thick of the drama, serving as the narrator, was always going to be a jarring plot point. Having her be hyper-nosy, hyper-sleuthing and hyper-unreliable was also always going to be a lot to take in as a viewer... but between the plummy generic British accent and needless swivel-chairing of suspecting absolutely everyone, to their faces, while giving us zero reason to accept Ani's innocence as a given... meh. Perhaps if she's given better material in Season 4 she can show us what she's capable of, but I think she was an unsuccessful addition to a stellar cast.
Tony - I just don't feel the god DAMN it wannabe disapproving Dad persona. It's patronising, and it made it hard to get as invested in the deportation of his family (not helped by the much better portrayal in Orange Is The New Black's final season as a recent comparison) - none of his scenes made me feel much.
Montgomery's gay struggle - the idea is good on paper but the way they executed it wasn't given anywhere near enough time to settle in before they'd Bury Your Gays'd him and framed him for murder for being a bad seed. That said, the way they ended the final episode implied that Season 4's strand could be to expose Ani et al for their conspiracy which might correct that bad taste a bit... but yeah, to me it just felt like Monty in Season 2 was a beta character poised to take on the chief antagonist role from Bryce; and then spent much of this season still being a beta character but suddenly given a queer coat of paint for two scenes, a brief macho-dad-rejects-son scene and then killed off-camera and exploited in death to give everyone a happy ending. Not quite as slick as it was gearing up to have been.
The reveal of who killed Bryce - the run of episodes right up to the moment where Zack tells Alex he's responsible went at breakneck, breathtaking speed and then the wheels came off in the final stretch. Zack having his leg broken in the riot but being in a brace and able to drive to the pier in the same time-frame as Bryce leaving the game and getting back to school? Jess being home and Justin inexplicably not being with her when she'd been molested on the field? Montgomery wanting to go after Bryce but conveniently overcoming his self loathing to go have a gay moment of whatever? Alex feeling guilty for walking away from Bryce, going back to help him and then shoving Bryce into the water for... pulling a face at Jess for being all for walking away and leaving him to die? They could, and should, have dropped the storyline where Alex and Bryce are chummy for a bit, and found a way to make them further at odds with each other so that Alex's split second decision to shove him into the harbour and then be clinically fine with being a murderer (bouts of anger in the boxing ring aside, obviously) make some sense. Like, have them be at odds mid-way through the season and then Alex have a "whatever dude, you're awful" apathetic last word against him before he accompanies Jess to the pier so that nonchalantly choosing to take his life doesn't seem so totally jarring. And why, when the police were militantly trying to frame Clay for murdering Bryce, were they totally fine with Zack 'only' beating him to within an inch of his life and happily going 'nah you're good'?!