Parts of the fandom got in a tizzy when Isshu's English name was announced to be Unova. Black is just calling it New York, probably to skirt around the issue.
The change in format and Genre Shift into Ho Yay-fueled cross-dressing parodies. Some find it hilarious, unique, and creative, that greatly improved the series, . Others find it tacky, an Overused Running Gag, and argue that the story just sank into annoying Fanservice.
Any time POD appears on-screen, the comments explode. He was even given his own slot on a character popularity poll; the only other characters to have their own slots were Black and N (understandably), with Ingo and Emmet sharing another slot, being Ensemble Darkhorses from the original games.
The shiny Litwick in Episode 21 is gained a following fast enough to start the possibility of Black catching her. Artist!Black is aware of this, and drew a gijinka version of it. She even has a name.
Fan Nickname: The Kami Trio contains Thundhurrus, Landorkus, and Tornadeuce/Tornerdus.
Harsher in Hindsight: All of those funny comic strips involving N's Zorua, one of them being an April Fools joke by N where it transforms into a kid that could easily be N and Black's son? When Black winds up in the Team Plasma castle, you find out that it was so severely abused that it stopped wanting to be a Pokémon and transformed into a young hybrid of N and Black so that it could be with them after Plasma's plans came to fruition.
In the story, Thundurus attacks Nimbasa City as well as the main character. In Pokémon Adventures, which the author is a fan of, the former doesn't happen, but the latter does. It happens right after Black's gym battle against Elesa, to boot.
The comic depicted all three of the Kami Trio being in control of Team Plasma, just like Pokéspe.
Cheren's Broken Pedestal towards Alder, which happened to Trip in the anime due to Alder becoming senile and unserious. And again with Alder! This time the anime Alder never remembers Ash and Trip's name, much like in the comic he never gets everyone else's.
Now that N is officially in the anime, he's pretty much tagging along Ash and co. just like he does with Black in the comic.
Kcalb, with the way he caresses Black's face, then shoves his hand into his mouth when it seems like Black is going to scream again. Methinks the author of this webcomic reads a lot of Bleach fan fiction, and took some inspiration from the popular Ichigo and Hollow Ichigo ship.
The Scrappy: White is beginning to generate quite a bit of hate from the fanbase for her accomplishments. Despite being The Ace as the point of her character. The fact that we don't get to see much of her during the story doesn't help matters either.
Squee!: The comment section's reaction to Black revealing his underwear to Tornadus. A few of the Pokémon commenters even proceeded to fight over him.
Squick: N is 21 (and a half). Black is 16. This becomes especially squicky when one considers that N started out as being Black's Stalker with a Crush and emotionally manipulated him into their current quasi-relationship.
The ending of episode 24, Zekrom refuses to select N as the hero and leaves before Black gets there (though by Zekrom's dialogue he isn't the hero either). Eve proceeds to verbally insult him as he cries at his failure until Black, Bianca, and the professors arrive and begin arguing with Team Plasma until N yells at them all to leave except for Black. The episode ends with N sobbing his eyes out while Black attempts to console him. Jesus.
The Woobie: N's getting his moments now that we're starting to see that his dad abused him and used him as a pawn for his egotistical plots.