- "Rebel Resolve" sets up Mustafar as being the planet where Jedi go to die... but in "Fire Across the Galaxy," nobody sets foot on the planet, and all of the action of the episode takes place in its orbit. As with the case of Liresan and Ryloth, the production crew likely didn't have enough money in the budget to show the planet's surface. Of course, given what Rogue One shows us about what (or rather, who) is on Mustafar, there are very good reasons not to go down there.
- Promotional videos for "The Siege of Lothal" showed Vader attempting to force Ezra to decapitate himself with his own lightsaber, and the blaster part of it seemed to be aimed perfectly towards Vader in the camera shot, suggesting it was to emphasize that Ezra was going to get out of it by surprising Vader by switching into blaster mode and stunning him, causing shocking results. Instead, Kanan jumps back into the fight and distracts Vader like in a normal fight.
- The favor Ezra owed to Vizago at the end of Season One. The writers could have had Vizago ask Ezra for anything, from help smuggling something with that could be used or used by someone with heavily morally ambiguous intent to assassinating a rival (with lots of moral issues in between for Ezra). Instead, they had him use that favor to have Ezra free him from being locked in a closet after his ship was hijacked by Hondo. Hardly the best use of a favor from a Jedi.
- The Ghost and the rest of Phoenix Squadron having to escape the Empire in "Legacy" is completely ignored to focus on Kanan and Ezra getting to Lothal.
- One of the trailers for Season 2 stated that Ezra's parents had escaped from prison and followed up with Ezra telling Kanan and Hera that he has to look for them, implying that the season's conflict would be Ezra being torn between staying with the Rebellion or searching for his parents. Turns out it was a case of Trailers Always Lie, because the line was edited to that from the revelation of their deaths in attempting to escape, but many have agreed that what the trailer suggested would have been a better and interesting alternative.
- Similar to the Mustafar case, after the struggle of trying to get to Lirasan in "The Legends of the Lasat," we don't actually get to see Lirasan in all its glory and we are instead told by Zeb of its state. This may be somewhat justified however, given that the show has a limited budget (compared to The Clone Wars, which, according to Word of God, cost several million dollars to animate per season), the most likely reason is that the production team simply couldn't afford to animate a brand new planet that would only show up for one scene.
- Darth Maul vs. Darth Vader was highly speculated once the former debuted in a Season 2 trailer, and Dave Filoni himself teased the idea. In the second season finale, however, Maul admits he's no match for Vader alone and the two never cross blades.
- For those who are unaware of the Servants of the Empire books, Zare's plotline from "Breaking Ranks" can come off as this. And for those who have, they may find The Reveal that Dhara did not become an Inquisitor, but rather was enduring torture in an attempt to turn her into one somewhat weak.
- The power struggle within the Inquisitorius is more touched upon out-of-universe than in-universe, and is never mentioned again after "Always Two There Are" aside from the Inquisitors' bickering for the rest of the season.
- In "The Antilles Extraction," Sabine is sent to infiltrate an Imperial Academy to help Wedge and Hobbie defect. This would've been the perfect opportunity to reveal what caused Sabine to defect or at least give us some more insight to her past, but it receives nothing more than an indirect mention that was nothing more than a throwaway line.
- Past "The Holocrons of Fate," it has been noted that little time has been devoted to exploring how Kanan's blindness affects the missions and his dynamic with the crew and thus is not really a dignified approach to disability. Other than having a few subtle gestures of an accurately vision-impaired person, Kanan virtually gets around like an able-bodied person and is even seen manning the Ghost's guns with no development to how he re-exercised this ability. Fans argued that "he got stronger in the Force" is a cheap Hand Wave and shortcut.
- The dynamics of Kanan's blindness is revisited in "Ghosts of Geonosis", specifically when Kanan has to completely rely on the Force so that he can keep a falling bridge up long enough for Saw and Rex to walk across, as well as a minor Tear Jerker moment where Sabine uses her Jet Pack and has a Curb-Stomp Battle against the Rocket Troopers, as Kanan isn't able to cheer on for her alongside the others since he doesn't know what she's doing. It's also the first time a character, Saw, outside of the Ghost crew gives subtle but visible cues of reacting accordingly to Kanan's blindness.
- "Ghosts of Geonosis" was expected to have Saw get poisoned by Geonosian insecticide, as said in the Visual Guide for Rogue One... which surprisingly doesn't happen or the poisoning already happened off-screen. However, FPJ later said that Saw will return, and it's entirely possible we may see him again return to Geonosis and get poisoned there.
- In the same episode, Zeb does not confront Saw about his brutality and how it affected Kallus. Entirely justified, however, because by the time they share screentime, everyone was already getting on Saw's case about his issues and they also had the situations of Klik-Klak, the investigation, escaping Geonosis, and avoiding capture by Imperials on their hands, leaving Zeb's confrontation to be inappropriate. In addition, Saw likely does not remember or was even present when Kallus's unit got executed. Ultimately, a confrontation is better suited for the Mercenary should he appear in the show.
- Fans agreed that they would've liked previous scenes that expanded on Hera teaching Ezra how to pilot in "Secret Cargo."
- Maul only shows up for three episodes in Season 3, with one episode reintroducing the Darksaber and his ties to Mandalore from back in The Clone Wars. When it was revealed that Saxon was with the Empire due to being an Opportunistic Bastard, people wondered what would happen, in combination with the Sabine's mother being Rook Kast theory, if Saxon, Kast, and Maul were to meet again, as well as Maul stirring up more trouble on Mandalore, which would also mean that Maul would've been enemy of not just Kanan and Ezra, also Sabine. Ended up not happening, because Maul has moved on from Mandalore after all these years and soon dies, Kast is not Sabine's mother and still has an unknown status in this part of the timeline, and Saxon dies soon after Sabine returns to Mandalorian Space.
- Promotional material suggested that Hera and Thrawn would've had a rivalry, and like how Kanan's rivalry was to the Grand Inquisitor, it would've caused character growth for her. This is touched upon in "Hera's Heroes", but is left alone until "Zero Hour", when Commander Sato dies and Hera has to take up the mantle. Upon seeing it happen in "Zero Hour", many are hoping that it continues into Season 4 and leads into Hera getting promoted to General as she is in Rogue One.
- Similarly, the ending to "Iron Squadron" where Thrawn and Sato acknowledge each other sounded like the two had crossed paths in the past and that there would be a rivalry between them, but judging by the lack of further comments on the subject, that moment was nothing more than an exchange of greetings and no rivalry festers between them either.
- With an endgame in mind for Kallus at the end of Season 3, there have been complaints that his characterization before "The Honorable Ones" never had any sort of foreshadowing that Kallus' morality was grey and instead quite the contrary in that he seemed to be a completely bad person. Not helped that due to a Time Skip between "The Honorable Ones" and the next time we see him as an Imperial with faltering loyalty that has undergone a HeelFace Turn and is now The Mole, it means that we'll never see the character development of how Kallus got from the ending of "The Honorable Ones" to where he is in Season 3.
- Thrawn says that he's plan to Feed the Mole upon discovery of a rebel spy in the Imperial ranks, it being Kallus as he finds out later. Due to the rebels expressing mistrust towards the spy after discovering their true identity, some were hoping that Thrawn's Feed the Mole plan would've resulted in the rebels coming to trust Fulcrum during an urgent time, but are instead put in a life-threatening situation due to being given false information and assuming that Fulcrum had double-crossed them, causing the rebels to sever ties with Fulcrum and leading to a Gut Punch considering what we've seen Fulcrum gone through the entire season. Instead, realizing the rebels are about to attack Lothal and needing to find the location of Chopper Base immediately, he talks to the other Imperials about doing this while Kallus is in hearing range, causing Kallus to accidentally lead him to where he makes his Fulcrum transmissions, allowing Thrawn to trace the signal's path and use that information to find Chopper Base. Considering every time he brought up his Feed the Mole plan, Kallus was in earshot, so it's possible that Thrawn used it as a Red Herring.
- Some were hoping that Yularen, now a high-ranking Imperial officer involved in Palpatine's conspiracy, would cross paths with his former colleagues Ahsoka and Rex, who are both now high-ranking rebel agents. A possible meeting between Ahsoka and Yularen was rendered impossible as Ahsoka goes MIA at the end of Season 2, but Yularen and Rex are within meters of each other in "Through Imperial Eyes". Though others didn't really mind as it would've taken the spotlight away from Kallus, Yularen was already involved in Kallus's and Thrawn's stories to be involved in another, and it has also been argued that Yularen and Rex might not recognize each other.
- In the Clone Wars Rex and Cody were shown as close friends and battle partners and in the Legends, continuity of Star Wars Cody continued to serve the Empire even after most clones had been discharged. It would have been interesting to carry this over into the new canon and see Rex and Cody meet for the first time in years only for both of them to be on opposite sides with Cody possibly seeing Rex as a traitor. Sadly the show ended before we got a chance to see this possible outcome.
- Zeb is absent from "Heroes of Mandalore", where it turns out that Sabine created a disintegration weapon and it ends up killing much if not all of her extended family, similar to how the ion disruptors were used to massacre Zeb's people, which could've allowed some development/insight on Zeb and Sabine's relationship.
- Similarly to "Ghosts of Geonosis", while Kallus speaks of Saw in a very bitter tone in "In the Name of the Rebellion", the pair never get a chance to meet each other in person, denying Kallus the opportunity to confront Saw directly.
They Wasted A Perfectly Good Plot / Star Wars Rebels