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.
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.
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.