- The ending to the IDW Publishing comic. Many fans see it as a letdown and not a satisfactory ending due to concluding with Jack and his allies planning one final assault on Aku's domain and leaving it open to interpretation whether his attack was successful or not, but there are some who consider it a decent enough finale, at least until the revival aired.
- When the second episode of the fifth season aired there became a split with the show's use of blood and gore. Some felt it was appropriate what with the show's newfound maturity and putting in more blood let the show heightened the stakes by showing Jack wounded. Others felt that the show is entering into the faux-maturity that plagues certain young adult media wherein the creators are trying too hard to be Darker and Edgier. A third group disregards the debate on maturity and argues that the blood worked with the striking stylized aesthetic of the show. And a fourth group has looked into the issue and realized that the show had been attempting to incorporate blood and even swearing all along but the daytime censors weren't allowing the inclusion of these things (scenes cut from "The Tale of X-49" prove that they were trying to add profanity and blood even back during the original run).
- A humorous one is when Jack loses his Badass Beard of Sorrow after he finally regains his sword. The fans are already thinking it subverts the possible future where he had one with his sword, while another camp liked his classic look, as this shows. Solved now that this future has been Jossed from happening due to the destruction of that time portal, but no doubt some people are now sore for a new reason- that the Guardian was revealed to be Dead All Along after the 50-year Time Skip.YouTube Comment: What?! But he's supposed to have the beard! IT WAS FORETOLD!
- Over whether Jack and Ashi should be paired up romantically or have a father/daughter relationship. The eighth episode (XCIX) finally confirms as a romantic relationship, breaking the base even further. There are three general groups: those who dislike the ship because they feel it came out of nowhere and/or aren't comfortable with the age and experience difference, those who like the ship because they believed it was foreshadowed properly since the first episode and/or believe that Jack deserves to be with someone after his unhappy love life (Ikra and the girl from his past come to mind), and those who don't care.
- Even putting Shipping aside, "Episode XCIX" was very divisive, being a lighthearted and comedic episode that turned out to be mostly Filler. Detractors feel that the episode clashes with the revival's Darker and Edgier tone, that the creators shouldn't be wasting time on inconsequential Monster of the Week plots three episodes before the end of the show, and the Jashi romance, if it was even needed, could have easily been fit into a more plot-relevant episode. Supporters argue the episode is a fun Call-Back to the sort of wacky adventures Jack had in the original series, its placement in the season is justified given Jack's He's Back moment in "Episode XCVIII" and there is still plenty of time to wrap up the main plot in the remaining two episodes.
- The Series' Grand Finale has already received some criticism from many fans due to some claiming that the entire episode felt completely rushed (not helped by the fact that the episode itself really was about 4 minutes shorter than usual by burning up time on the intro, a Mythology Gag to the old intro (though a heartwarming inclusion of the late Mako) and an Overly Long Gag where the Scotsman rattles off the names of most of his daughters) and anti-climatic. There's no tearful reunion with Jack's parents, which is quite jarring to witness considering how long he's been fighting to save them. Not even a proper send-off for all the characters of the future Jack has befriended. And then there's Ashi's death/Cessation of Existence which didn't really sit well with others. Despite many other fans saying the ending was satisfactory and was a proper conclusion to the series as a whole (in agreeance with the creator happy its finally over for him). The biggest point of division seems to be Ashi's death, which some see as pointlessly cruel to Jack (it happened on his wedding day no less) and others see as a lead-in to a poignant conclusion to the series. It's also been criticized for the sheer amount of Idiot Ball moments from Aku in order to cram the conclusion of what should have been a much longer season into 22 minutes.
- Another one is whether Greg Baldwin did a good Aku or not. While Mako's unfortunate passing made recasting the character necessary, some didn't like Greg Baldwin's deeper voice, and think he gives but a pale imitation of Mako's performeance. Others are not only fine with it, but think he's at least a worthy successor in the role.
Broken Base / Samurai Jack