Episode 1 of Season 3 shows signs of hostility between the new allied planets and the Blade of Marmora due to racism against the Galra. This plot thread is all but forgotten once Lotor shows up.
Some fans who don't view Lotor as a Jerkass Woobie felt that it should have been Acxa, Zethrid and Ezor who prevented the destruction of Naxzela and saved Keith from his kamikaze attempt in the Season 4 finale instead, given that they turned against Lotor after realising that he went too far on his plans to gain more Quintessence and how shocked and sad they were after he killed Narti in the antepenultimate episode of the season.
Keith temporarily leaving to join the Blade of Marmora. The fact it occurs only an episode into Season 4 with little build up is considered a waste, but the fact Keith was Put on a Bus also doesn't help. Instead of seeing Keith's training or his pursuit of Lotor or even him coping with the issues that made him leave the team, he only really appears at the beginning and ending of the season.
On a related note, Keith's leadership arc in Season 3 becomes a "Shaggy Dog" Story after Shiro regains his partnership with Black. What was set up to be a struggle for Keith to step up to the plate and work on his relationship with the others becomes an exercise in angst after he starts abandoning the team for the Blade and ultimately quits Voltron. Luckily, in Season 6, Keith returns and gets to finish his leadership arc. Nevertheless, some fans still feel this trope applies as all of Keith's character development was achieved offscreen in the span of a brief timeskip montage.
Many fans felt that Lotor actually being Good All Along would've made a better storyline for the show than him being Evil All Along, given that the character was on course on being more heroic than his original Voltron and GoLion counterparts before said reveal, not to mention fans were left disappointed that he never got to tell his side of the story about the harvesting as he was flipped out by Allura after Romelle told her story about it to the team.
Inverse to the above, Lotor had the chance to come across as a rather complex villain whose ruthless ideas about preserving Altea could have been genuinely thought-provoking, especially compared to Keith's unwillingness to sacrifice Shiro for the greater good, and whose eventual downfall would come about more organically. Instead, to quote Word of God he goes "full Azula", and as a result becomes more akin to the Saturday morning cartoon villain of the original series.
In Season 5, Lance gets a message from the real Shiro on the astral plane, leading fans to speculate that Lance was going to figure out the deception and tell the team, then the team would round up Keith and go to the rescue. Many speculated that this would be key to the "growth" of Lance's character that the showrunners were constantly talking about in the run up to Seasons 5. Instead the team remain oblivious until Keith's return. The clone is exposed not through any kind of deduction on the team's part but through Haggar forcibly brainwashing him before their eyes, followed by Keith taking him down and rescuing Shiro more or less singlehandedly, and Lance's main contribution to the whole issue was realizing the significance of the message too late, and lamenting that he should have noticed that something was wrong.
On a related note, aside from one offhand comment, the show never explores the ramifications of Shiro in seasons 3-6 being a clone. The fact that Shiro now has all of Kuron's memories had to be addressed in an interview as no such thing is touched on within the show, nor is there even an opportunity to do so. Neither is there an exploration of his sudden loss of ability to pilot the Black Lion (which also had to be explained in an interview), his response to being cured of the mysterious disease that affected him in his early life, or his PTSD resulting from his time as a Galra prisoner that was a focal point of his arc in the first two seasons. Likewise he is the only main character not to have his family shown, due to his backstory getting cut from the show.
Season 3 introduces Lotor and his generals as a close-knit and competent group, and later reveals that Lotor was building his own ships out of a second comet made from the same material that was used to build Voltron — ships that look suspiciously like body parts capable of assembling together. While it turns out that those ships were used to form Sincline, the buildup to Lotor's team piloting it as an Evil Counterpart of Team Voltron appears to have gone nowhere after the death of Narti, the rest of the generals turning on Lotor, and Lotor piloting Sincline by himself.
The Voltron Coalition, whose formation was a major focus in Seasons 3 and 4, largely disappear after Matt's attempt to liberate his dad. Potential friction between them and the Paladins for aiding Lotor after he became emperor of the Galra would have made for an interesting plot, but it goes completely unexplored. Worse still, in Season 7, we hear that they're being hunted down by the Galra remnants after Lotor's disappearance, and don't learn of their fate until a massive cameo in the season finale.
The Bayards, and the properties thereof. Only in the final season do we learn what they even are (weapons made from the same material as Voltron itself), and none of the Paladins are ever capable of using them to the extent of Galra Royalty, despite Lotor using the Black Bayard with the same effectiveness as Zarkon despite not even being a Paladin, and despite Zarkon pointing out in the first season that one's skill with the bayard was emblematic of one's skill as a paladin. After Keith risks his life attempting to retrieve the black bayard for Shiro in the first season, and after Shiro successfully retrieves it in the second, he is never seen using it in combatnote This is probably because Shiro was originally supposed to die in season 2 and so they never created a bayard weapon for him even after he came back..
The Entity is introduced very early on in Season 3 as a dark corruptive force of Quintessence partially responsible for Zarkon and Honerva's turn to darkness. It returns in Season 8, where it possesses Allura instead, seemingly setting her up for a Face–Heel Turn of some kind, becoming the final villain. All that it amounts to is being briefly used as a tracking beacon for Honerva before being suddenly dropped altogether as if it never existed, and no explanation as to where it even came from.
