Tonraq advising Korra to be careful about telling others about her relationship with Asami. Is this born out of genuine concern for his daughter and how people might see her, or a desire for her to conform to traditional Water Tribe ideas regarding same-sex relationships? Or perhaps it's a combination of both?
Anvilicious: The comics are not at all subtle about the idea that homophobia is bad, with several characters explaining to Korra and Asami the various forms it takes in the Avatarverse (information that they, as people who live in those cultures, should already know). What makes these scenes especially jarring is that despite being warned throughout Part One that they will encounter homophobic backlash, Korra and Asami never actually do.
Part 1 focuses pretty heavily on Korra and Asami's relationship and what exactly led up to it as well as the aftermath, which has made many fans happy due to many feeling that their relationship in the series was rushed.
Bolin has joined Mako on the police force, after many fans pointed out that as an earthbender, he made far more sense in this role than his brother in the first place. However, he does leave the force again at the end of Part 3.
The Triple Threat Triad, after many fans' complaints about them spending the entire series being a wasted presence and laughable jokes, finally take a level in badass and are given a chance to shine.
Evil Is Cool: Tokuga hits it just as hard as the Red Lotus, from the opposite direction of being a Badass Normal who can go toe to toe with any bender and was able to bring all of Republic City's criminal gangs under his control through sheer awesomeness. It takes Bolin breaking out his lavabending to put a dent in him. And at the end of Part 1 he becomes an Empowered Badass Normal. Part 2 continues this in establishing himself as a Visionary Villain that commands obedience by fear, set a trap that both predicted and nearly killed the task force if not for Mako's quick thinking/bending, gave Korra a run for her money in a one-on-one fight and won via hostage situation that ended with the triad marching off with military-level equipment! Tokuga, welcome to the adult table with Amon, Zaheer and Kuvira.
Evil Is Sexy: Jargala. A smooth-talking, badass Big Beautiful Woman with similar eyes and make-up as Asami that practically has flirtatious undertones with Asami in attempting a protection racket and leaves just as smoothly as she arrived. It's like she's the age-appropriate answer to Azula and then some.
Harsher in Hindsight: Remember in "Korra Alone" how Korra felt insecure being compared to the last Action Girl Avatar, Kyoshi? Well aside from Kyoshi's Cerebus Retcon, that's now quaint compared to Korra now feeling hopeless that even with Kyoshi's famed accomplishments and long lifetime, she failed to affect change in her homophobic homeland and fears the same treatment. Considering Korra's own accomplishments to date, that's seriously saying something.
Informed Wrongness: Raiko's decision to fortify the spirit portal at the start of part 2 is treated as wrong by Korra, who fears it'll cause another breakdown in relations between humans and spirits. Except that by this point the spirits are implied to not want any more visitors coming through the portal - a deduction Korra herself had come to - and no-one ever asks the spirits for their opinion on the portal. Furthermore, by that point the Spirits have shown themselves to be actively hostile, mutating Tokuga and attacking humans who come near with little to no provocation, and show no interest in trying to communicate with the humans to tell them what their problems are. For all that's said in the comics, Raiko arguably did the spirits a favor, and even if he wasn't, he was still doing the right thing to keep people away from the incredibly dangerous creatures that are immune to conventional weapons and are capable of twisting your body in hideous ways with a touch.
This extends to Part 3, where Raiko's plan to combat Tokuga by provoking him into traveling towards the bay, where he can be shot down by the military is seen as an act of cowardice. Granted, most of the characters weren't privy to this plan, only seeing Raiko leave the area out of fear as far as they were concerned, but even those privy to his idea saw it as bad, since it would result in the death of his hostages. However, in the off-chance that Korra's rescue attempt failed, Raiko's plan really does come across as a solid strategy that would have done a lot to lower potential causalities from a poison gas attack.
Raiko not only tries to turn the public against Korra to distract them from the reasons theyre angry at him, but it's implied that he withheld food from the refugees just to screw Zhu Li over out of spite, even though Zhu Li did nothing to antagonize Raiko in the first place. Even the fans who defended him up to this point have a hard time here.
How does Tokuga plan to take control of Republic City? He threatens to release a cloud of poison gas on the populace if Korra and Raiko don't do as he says.
Korra and Asami's intense moment in the latter's office in volume 2 looks like this to some readers. The dialogue is reasonably strong, but Asami's face is so weirdly drawn, with her eyes too big and bulging and other issues, that it can come off as just silly, rather than the serious romantic interaction it deserves to be. To be more specific, the frame that's supposed to be a Held Gaze with Asami angled down toward Korra's eyes yet she instead appears to be staring at Korra's hair then by the following frame, Asami's pupils are just as green as her irises.
Fire Lord Sozin outlawing same-sex couples. While this scenario is true enough to real-life authoritarian nationalists (just look at pre-Nazi Germany or pre-European-interaction Japan, for example), the fact that the nation is stated to have been tolerant specifically until he came along, as well as having all of his political enemies (except the Earth Kingdom) being tolerant of it, just makes it seem like he was evil for the sake of being evil. Along with the following comment from Korra ("That guy was the worst!"), it can also come across as trivializing the fact that he killed off all the airbenders (except Aang), initiated dragon hunting (which killed off most of the first Firebenders), and refused to save one of her previous lives (Roku) purely to allow his plans of conquest to go forth.
The spirits are openly unhappy about the new spirit portal, but, despite their grousing, Korra refuses to close it and they concede they have no choice but to accept her decision. Korra even brings up that they were all too happy to keep out of Kuvira's attack on Republic City, which is ultimately what led to the portal's creation. While not quite Laser-Guided Karma, it's satisfying to watch the obnoxious spirits be stuck in a situation that they hate, especially since they honestly can't say they didn't bring it on themselves.
For those who don't like President Raiko, he gets stuck with a 0% Approval Rating, with his numbers in the upcoming election being -3 despite having no opponent. Not only that, the comic seems to intentionally try to make him as unlikable as possible. And come Part 3, he gets replaced as president by Zhu Li.
Unintentionally Unsympathetic: When Tonraq suggests that she and Asami keep their relationship low-key for the time bing, Korra makes an angry outburst at her parents calling them "narrow-minded" and "insensitive". On the contrary, Korra's parents were actually shown to be happy for Korra, and were more concerned about how others would respond, which was understandable given the conservative traditions of their tribe. Yet Korra's treating them as if they were the bigoted ones.