Arc Fatigue: Apparently, many of the fans got fed up with this arc, as it takes an awfully long time for anything resembling a plot to really kick in. It's first hinted at in episode 14, and only gets going by episode 22, with only 3 episodes in the whole series left after that. This was made worse when the build up didn't really lead anywhere. Just a team up for the old characters to beat up some mooks, and the generic shonen lead to defeat the generic villain in an anti-climatic duel.
"Tagiru Chikara", the insert song that plays when Gumdramon evolves from the first time, is pretty great in and of itself. Bonus points go to the fact that it's done by the one and only Psychic Lover, of Tokusatsu fame.
Meanwhile, the jazz Leitmotif that plays when Astamon makes his appearance was immediately noticed by fans. Bonus points go to them for using musical stylings that are evocative of earlier series.
In episode two, the original version of "We Are Xros Heart" from the previous arc makes its glorious return.
And of course, you can't leave out Yuu and Damemon's theme, "Shining Dreamers", which played for the first time during Damemon's return in episode five.
Nene's rendition of "New World" and "Stand Up" in episode ten are pretty impressive.
Episode fourteen brings back "Blazing Blue Flare" as Kiriha and ZekeGreymon lay the smack down on Volcdramon.
The song celebrating the series' anniversary, Legend Xros Wars, is not only awesome, but beautifully nostalgic as it incorporates elements from all the previous series.
Big Lipped Alligator Moment: Archelomon, of all people is present at the gathering of the heroes after Quartzmon's death at the end, despite not being seen in the season at all beforehand.
Critical Dissonance: Regarded by many of the fandom as the worst season of Digimon, Young Hunters somehow managed to receive a nomination for Best Animation at the 2012 International Emmy Kids Awards, which it (un)fortunately didn't win.
Designated Hero: Tagiru makes it clear that he's in it just to become a superstar, and at times so does Gumdramon. Even when Earth is in danger of being destroyed after Quartzmon merges with it to allow DigiQuartz to rapidly expand and take over, they're still more concerned about becoming superstars then the fact that you know, everyone they know and love is being assimilated into Quartzmon.
Fanon Discontinuity: Some fans think the previous arc of Xros Wars had a decent ending with the defeat of Bagramon and consider Hunters a poorly written and unnecessary addition to the series. Among the most common complaints are the Monster of the Week action composing most of the episodes and the new main character, who is seem by many as too generic, uninteresting or just plain annoying, receiving too much focus and overshadowing the rest of the cast with no noticeable or long lasting development. In fact, many people only watched it for the crossover finale and even there Tagiru managed to fight the final battle alone.
Ho Yay: Between Tagiru and Yuu. In episode 16, when Yuu and Tagiru are trapped in a phone booth together and a girl finds them with their arms around each other, they say that they are "really good friends". They were trying to divert suspicion, but still...
To a lesser extent, there are those who liked the original Xros Wars and only watched this series for the returning members of Xros Heart, who sadly don't get a whole lot of screentime.
Magnificent Bastard: All three rival hunters have tried their hands at being this, to varying degrees of success. The one who comes closest in the end is Ryouma, who is actually under the control of Quartzmon and is part of the Big Bad Duumvirate with him, and who manipulates and backstabs the other characters masterfully without them ever catching on until it's too late.
Quartzmon himself then outshines him when it's revealed that he's technically been Ryouma's Digimon partner this entire time!
Misaimed Fandom: In a strange case of the show not helping it's case, this season was meant to be about Tagiru's self-growth to becoming a leader, rendered moot due to the lack of usual plot most of the season, Tagiru's Static Character, and the old leaders coming in, causing people to be more excited about that, than what the arc was about.
Betsumon seems to attract a lot of hate from fans who find him just plain irritating.
Along with the former being one of the most hated protagonists in the Digimon franchise, Tagiru and Gumdramon are also Replacement Scrappies for Taiki and Shoutmon, respectively. Did you think the hatred for Davis was bad? You've seen nothing compared to the sheer level of loathing that Tagiru gets from some fans for quite a few reasons including his incredibly selfish motivation, unchanging character and constant spotlight hogging which both result in nobody else apart from characters of the day gaining character development, how everything seems to go in his favor in the end, his unbelievable degrees of idiocy, and most of all getting to fight the final battle alone and being the only one to have a proper goodbye and reunion with his Digimon Partner.
Astamon being Quartzmon was also a little left field, considering he hardly said or did anything
They Changed It, Now It Sucks: Rather ironically, there were a few people who were angry that the series seemed to be dropping DigiXros, after the concept itself was subjected to this trope. Come the preview for episode two, we found out that DigiXros was still part of the show anyway.
Yuu and Damemon are Ascended Extras who are somehow simultaneouslyDemoted to Extra. While there are a couple of episodes that focus on Yuu, Damemon gets even less attention to the point where he's practically a Living Prop in some episodes.
All three rival hunters. We never get any background information on them (what their family lives are, what motivated them to become what they are now, how Airu and Ren met their partner digimon), nor are they all that developed personality wise save for Airu (and Ryouma in the last few episodes). For many, this was disappointing due to their initial potential.
As mentioned above, this series could have been a new opportunity to work out Dagomon as a powerful antagonist like a true lovecraftian digimon deserves, unlike his aborted role in 02. However, he only appears as a curiosity and is fastly forgotten.
They Wasted a Perfectly Good Plot: No, there is no time-travelling, at least from the audience's perspective. Many feel the Grand FinaleCrisis Crossover was vastly underwhelming. The five previous leaders were reduced to living batteries for the Brave Snatcher. Due to everyone getting reduced to DigiQuartz Tagiru is the only one to fight the final battle. At the end all the Digimon and humans are separated back into their separate human and Digital Worlds. Not to mention the open ending, and The Clock Man being Bagramon.
DigiXroses were rarely used in the arc, despite the subtitle. Most of the hunted Digimon never made appearances after their debut episodes, either for Xrosing or for fighting solo, and even the core members of Xros Heart besides Shoutmon hardly made appearances.
Seeing the generals and their armies unite a year later, the mystery behind Digimon inhabiting a parallel timeline feeding on human emotion, a competitive hunt for those Digimon inhabiting this parallel timeline, Gumdramon's development from delinquent to positive societal figure, the old generals taking on a new hunting role, rookies to the Digimon situation going into the hunting situation blind, a crisis requiring the meeting of teams from several continuities, each was an interesting premise on its own. Altogether, none managed to have their depth sufficiently explored or reach a satisfying conclusion in 25 episodes.
Tough Act to Follow: You know how Xros Wars was this to the franchise up to that point? This season is this to Xros Wars! And this series had THE worst ratings in the franchise history, too.