Long post ahead. I started writing this list of flaws in May 2016, I'm not sure when I finished it. I was so disgusted with Ep.9 I stopped watching and only caught up with the finale some 6 weeks later in August. I consider the last three episodes of S6 as the absolute worst in the series to that point. I never saw S7.
Season 6 was a disaster in terms of writing.
It was ruled by fan service, shock value and most of all plot driven character behaviour, as when Davos forgot all he was about and had come for when he decided to risk his life around the body of a man who had refused his king’s request for help and went to ask his main antagonist for help in reviving him.
Jon Snow had to be brought back, fan favourite Davos had to look good and the religious zealot Melisandre had to keep as low a profile as possible. Later on, as Davos was wanted to help recruit an army and participate in a battle, his questioning of Shireen’s fate had to wait patiently only so Melisandre’s vision of herself in Winterfell could come true.
Ep. 1 The Red WomanDavos is the first one up in the morning at Castle Black, he must have gone to bed early. All those who find Jon dead are his friends. Apart from them, only Melisandre comes knocking at the door.
Davos and Jon Loyalists have no reason to lock themselves up, they are not threatened. If Edd can leave, so can they. How come Davos would take party for the loyalists anyway? If he feared for his life as a witness, why not for Melisandre's? Jon Snow turned down his request for help in the S5 finale, he ought to see a change of Lord Commander as an opportunity.
Brienne turns up all too conveniently to save Sansa. Little trained Pod and broken Theon come through the fight against professional soldiers without a scratch. Brienne now has the power to make dogs vanish.
All too easy take over in Dorne. All the guards were on it, really?
Unexplained presence of Sand Snakes on Trystane's ship. How did they get there and past the crew?
Tyrion is walking "incognito" in the streets of Meereen after being seen sitting next to Daenerys in Daznak Pit.
Daenerys is brought to Khal Moro unmolested although no one knows who she is.
Arya is being trained as a secret assassin in plain sight on the streets.
Melisandre's "shocking reveal" is just that; shocking. It will have no bearing on following events in the whole season.
Ep. 2 HomeWildlings arriving just in time to save the day.
Tyrion specialises in cock jokes. Why is he so frightened of dragons on hunger strike? Not drunk enough?
Davos has no reason to ask Melisandre to bring Jon Snow back. He should be asking about Stannis instead.
Ep. 3 OathbreakerMelisandre is discarded as a used towel after Jon's return.
Sam puking in a pail.
Very unrealistic situation of Tommen going to the High Sparrow without being advised against it by anyone - this might have been explained by Kevan's support, which is hinted at in Ep. 6 but no further explanation of Tommen's behaviour would be given.
Ep. 4 Book Of The StrangerSansa should not have been able to get to Castle Black without trouble when Ramsay knew exactly where to look for her. There is no way the Warden of the North couldn't get the road to Castle Black blocked by others and further search parties started. Sansa arriving there unhindered was just pure fan pleasing.
Osha was sacrificed for shock value. She wouldn't make an attempt on Ramsay's life without an exit plan.
Daenerys trapping and burning the Khals is one of those obvious superhero moments which undermine credibility of the story telling. After seeing this, you know anything will happen to provide a pleasing or a shocking moment in spite of logic.
This episode is the openly over-feminist one, where all men are portrayed either as villains or as subservient to women. Loras, Theon, Jon Snow are broken men dependent on their sisters' strength. Men in active positions are "bad guys": the Master's emissaries, the High Sparrow, Ramsay and the ever ominous Littlefinger.
Ep. 5 The DoorLittlefinger not only moves around extremely fast, he also took Moat Cailin without difficulties, although the Bolton army had to go home by ship when it was occupied by a few Ironborn.
One more scene of Arya fighting with a stick, this is the fourth and now the Waif beats her without it. Is this woman real?
The Kingsmoot makes Euron and his followers openly support kinslaying then get tricked as mere fools. How does Euron know about Daenerys' alleged hatred for the lords of Westeros? She never claimed any of this. How is Euron supposed to build a fleet?
Sansa is sending Brienne to the Riverlands to ask for help and the improbability of it all is not even brought as an argument.
Daenerys sending Jorah away is nonsense as she is the person who can best help him find a cure. This is a tear-jerking scene for effect only.
Ep. 6 Blood Of My BloodSam's father is portrayed as a caricature more upset by having a wildling at his table than interested in learning about White Walkers.
Tommen was at the Sept and Jaime, Lord Commander of the Kingsguard, didn't know about it.
Daenerys conveniently happens to sense Drogon's presence in a way which enables her to surprise and impress the Dothraki.
Ep. 7 The Broken ManJon Snow, Lord Commander of the Night's Watch, tours the North asking for support in attacking the Boltons and no one calls him a deserter or an oathbreaker. Wildlings who "thought he was some kind of god" in episode 3 now haggle with him and need to be convinced by Tormund.
The rogue Brotherhood had no apparent reason to commit such a massacre, this appears to have been there only for shock value.
Arya strolled around Braavos to be surprised then escaped in spite of stabs in the gut.
Ep. 8 No OneArya survives and recovers in spite of falling in a dirty canal, then manages to keep ahead of the Waif in a pursuit worthy of James Bond, luring her into a dark place and killing her. Jaqen's statement that she has become "no one" makes no sense other than provoking the opposite answer purely for the delight of the audience.
The Hound is just a witty killing machine in this episode. Is this all he was brought back for? The character's actions used to have weight, now he is just fan service.
Nothing explains how Beric Dondarrion knows of a peril in the north.
The offscreen death of the Blackfish is just a way of getting rid of a no longer needed character. His decision to commit suicide made no sense when he was offered a chance to escape.
Brienne and Pod leave Riverrun in secret for the sole purpose of giving the audience a winking scene with Jaime. They had an agreement and left their horses in the Lannister camp anyway.
Yet another longish scene of Tyrion making smalltalk; the alert could have sounded in the first sentence but Tyrion needs something to do, anything. Daenerys returned just in time to save the world, so it will all be fine?
The whole "Waif vs Arya" chasing sequence appears to have been a pure action insert designed to produce a cliffhanger followed by a happy resolution without furthering of the plot or characterisation. The Waif's motives were never made clear.
Ep. 9 Battle of the BastardsMore superhero writing for Daenerys. Drogon always does just what she wants when she wants it. The other two dragons come out on their own at just the right time. Sons of the Harpy are killing normal people outside of the gates of a city under attack just so they can be conveniently slaughtered by arriving Dothraki.
The conversation between Daenerys and Yara is all about putting women in power and defeating men.
Jon Snow is portrayed as an emotional fool once again and Ramsay as a man shooting at his own men against all realism. Bodies pile up on the battlefield without visible explanation, the whole battle is more like a horror show than a plausible event.
The Knights of the Vale were said to have taken Moat Cailin before but Ramsay never seemed to know about it and was surprised at their arrival. Not only is this unrealistic since the place is known to have successfully defended the North for centuries, but it would also have been notified back to Winterfell and have caused a reaction. Roose said in S4E02 he had to sneak back into his own land because the Ironborn held it in earlier seasons and we saw Theon get it back with a trick.
Ep. 10 Winds of WinterLuring Lancel underneath the Sept serves no logical purpose. It is an artificial way of telling viewers what is about to happen and adding tension to the scene. His stabbing is in absolute contrast with Arya's: the "little bird" is more effective than the trained Waif.
Margaery realising the danger is implausible. The logical suspicion would have been that Cersei had fled the city. This is just another tension adding trick.
Arya travelling to the Twins, infiltrating the staff, killing two of Walder's sons and baking them while the the cook is away, really? Besides, she gave up on the gravy.
Sam and his stolen sword arriving just where he told his father he would and no one is coming after him?
Bran gets to the Wall and all he does is watch the end of the Tower of Joy scene?
Tyrion is telling Daenerys not to take her whore to court, seriously?
Jon Snow made King in the North in spite of being a Night's Watch deserter and having essentially botched his part of the battle against Ramsay. No one ought to follow such a "leader".
Are Cersei and Littlefinger becoming caricatures of themselves?