Alas, Poor Villain: Professor Rotwood may not have been the nicest character on the show, but seeing him brutally get injured in the episode "The Ski Trip" was really harsh. All he was doing was his job in making sure the students behaved on the trip and he gets repeatedly hurt.
Is Jake a human who can turn into a dragon, or was he a dragon raised as a human?
Rose's actions before and immediately after her Heroic Sacrifice could be subjected to this. When did she decide her course of action? Right after she was blackmailed, before she got the Huntsman the Aztec Skulls in Jake's possession, or was it a much more spur-of-the-moment thing, with her winging it throughout the battle? What did she mean when she told Jake she'd be okay? Is it that the safety of those she loves is all she needs to be at peace, or is it a lie to keep Jake calm? Also, why didn't she try to exclude herself from her own wish? Was she under so much pressure that she never even realized that was an option, did she not think it was possible, or was she suicidal to some degree?
Broken Base: Mainly concerning the permanent Art Evolution the series had. Even amongst those who like it there's debates about certain redesigns, like the Oracle twins.
Growing the Beard: The second season has been considered an improvement, thanks to a change in direction with Steve Loter. The art style is the controversial part, though many dislikers don't actually hate it. They just wish they had kept the original style or if the season 2 style had always been the art style.
Moral Event Horizon: The Huntsman definitely crossed this line in "Homecoming", when to finally carry out his master plan of genocide against all magical creatures, he forces Rose to betray Jake and help him by threatening to kill her parents.
As deserved as it was, the destruction of the Huntsclan, where all members are hoisted into the air, kicking and screaming, by their glowing Birthmark of Destinies and zapped to death.
The Scrappy: Huntsboys #88 and #89. Veered into Creator's Pet territory after the Huntsmen as a whole were killed off, but the two continued to appear anyway. Though they quit being Huntsmen at the last minute and weren't real Huntsmen in the first place.
They Changed It, Now It Sucks: In regards to the change in style for season two. Many liked the first seasons designs and felt season two's was way too abrupt and trying too hard to match their character's personalities. Some major examples include the Oracle Twins, the Huntsman, Counselor Chang, Eli Pandarus, the Dark Dragon, and especially the dragon forms of Jake, Lao Shi, and Haley.
Many still wonder the whereabouts of Rose's twin sister.
Fans have been curious about the remaining top 13 dangerous creatures/creatures of the magical world.
The Dark Dragon. We are given almost no backstory for him and learn almost nothing about him. It would've been interesting to see how he became so powerful, why he wants Jake on his side, and what his possible human form looks like. Come Season 2 he's treated like a Generic Doomsday Villain. Many also felt as though he was not quite as powerful as he was made out to be.
Fred Nerk would've been an interesting rival/ally for Jake, however he only made one appearance. This is especially lame since Word of God originally promised that we'd see more of him.
Other than the Huntsmaster, Rose, #88, and #89 we never really met any Huntsclan members formally.
Eli Pandarus could've been a good recurring antagonist, especially once he became more ruthless. Unfortunately he was only used a handful of times.
Yang Jake also could have been a good recurring antagonist. Him meeting Rose could have been interesting, at the least. He's only used in one episode, though, and it's implied that he's killed off at the end of that episode.
Similar to Fred Nerk, Nigel Thrall could've been a good ally or rival for Jake especially since they went to the same school but came from different magic lineages.
Chang's role as a double agent only lasted a few episodes before she abruptly led Lao Shi into a trap.
The Dark Dragon's role in the series. Nothing ever comes from his desire to conquer the magical world, convince Jake to become his apprentice, or much else really.
Related is the Dark Dragon's plan to gather an army of evil magical creatures to take back the world from humans. We never see any of his allies other than Chang, Bananas B, and his Shades. This would've provided a good opportunity to bring back some popular villains such as Pandarus, the Kelpie, and the Gorgon Sisters who all could've been recruited.