Alternative Character Interpretation: Both Team Rocket and Team Liberty fall victim to this, primarily in regards to their overall place and role in causing the Rocket-Liberty War.
Team Rocket has pretty consistently been seen as an evil—or at least more morally ambiguous—group, and for good reason. But are they necessarily evil, or were the majority of their actions—primarily in taking over the Kanto regions—an effort to correct flaws in the previous government and root out some sort of corruption? If so, were they justified in doing so, considering the deaths that occurred as a result of their actions?
Team Liberty ostensibly fights for equality and freedom, but they are also the primary group responsible for starting the Rocket-Liberty War, having been the ones to declare it against Team Rocket. Not to mention, their leaders' backstories mean that—at their most basic—the three are essentially a dog of war (Goldhawk), a rich fellow with no particular use for his wealth (Blackskull), and a League Champion inadvertently deposed due to rebellions from various Gym Leaders causing her title to be shut down. Was Team Liberty really created for benign reasons, or was it a means to an end by its founders?
Arc Fatigue: The Manaphy Arc, as a result of poor management, excessively common periods of downtime meant for character development that were all clumped together, and constant player punches, all ending in a much-bemoaned Anti-Climax.
Kane's takeover of Opelucid, which—while interesting—came at the same time as two of the Sins' introductions, splitting focus between the two and causing both to stall as a result of the three antagonists being managed by the same player. Real life issues eventually caused the player to go on hiatus from the game, prompting Parugi to take over and wrap up both.
The Liberty Ball is seen as having overstayed its welcome and paced itself poorly, though it's a mild example compared to the above ones.
By the time it finished, the Ancient Darkrai plot had been going on for something like three years real-time. Because of that and how much it affected the in-game world, it was considered a great relief when the plot finally ended.
Archive Panic: A noted obstacle among the populace, as Rise of the Rockets has been running for almost five years as of the time of writing and thus has an incredibly large amount of back story set up by now. Attempts have been made to mitigate this, with varying levels of success.
Awesome Ego: Sang, though this is perhaps because of the subversive nature of his purported narcissism.
Big Lipped Alligator Moment: The entire sequence involving Jake Soren and Jason Alco traversing through a parallel dimension inhabited by "the Entities," massive creatures representing different elements. Their inclusion to the story contributed virtually nothing to the game and has never been expanded upon, and Parugi has since declared it non-canon.
Parugi freely admits that Kyle's sudden possession of a gun and offer to kill Evan and Zach while trying to break Sonja out of her Heroic B.S.O.D. likely came off as this for many, even keeping in mind Kyle's Sanity Slippage up to that point. May have been intentionally invoked for this very reason, as it did turn out to be an odd enough situation to bring Sonja back to her senses and Kyle did spend some time questioning what had just happened afterward.
The existence of Keston Ail, Kyle's Enemy Without-slash-Enemy Within, particularly since it's ambiguous whether he actually existed or was merely a figment of Kyle's imagination. Unlike Feral Tierra or Shade or even the Sins, no real explanation has ever been offered as to how Keston came about.
The snowball fight in Unova could be seen as this, though it wasn't necessarily a bad thing.
Designated Villain: Team Rocket, primarily due to how forceful their takeover was implied to be and because of the public disturbances that their Mooks have caused. Contrary to popular belief, however, Team Rocket's reign has had a fair number of positive effects on the Kanto regions, and the Shadow Admins have made a point of stopping the trouble caused by their lower-ranking group members.
RotR has a tendency to introduce mechanics and story aspects that later appear in the mainstream Pokémon games, such as the idea of capture experience, which was introduced in RotR three and a half years before any of the games picked it up.
Moral Event Horizon: Shadow Admin Ace authorizing the reactivation of the Shadow Pokemon project, effectively allowing a group of scientists to perform unspeakable experiments on Pokemon to turn them into super soldiers.
Sabrina has one after killing Archie when she takes his Pokémon, still inside of their Pokéballs, and psychically crushes them, killing all of them as a result. It has since been revealed, however, that she has been under Mind Control by Rocket Executive Elton for some time, along with Surge and Koga, and so this may not have been of her own free will.
Rocket Executive Tobias Elton certain crossed it when he put Sabrina—as well as Surge, Koga, Ash, Tate, and Liza—under horrific experiments in order to control them, leading to the above.
Meghan Vert crossed it when it was revealed that she had been cloning Legendary Pokémon for the sole purpose of killing them and using their energy for her Power Suits.
All of the members of the Hojohsin League have arguably crossed it at one point or another.
Ford's willing to sic assassins on young Team Liberty agents or even a ''Darkrai'' on innocent children, as seen during his attempts on the lives of Jayron and Kyle for the former and Joker's children for the latter.
Pierce, though probably the most humane by now, is nonetheless implied to have begun executing numerous Team Rocket and Liberty agents in addition to imprisoning them, even following the very Rocket-Liberty truce that his group had been demanding up to that point.
Hayes bombing Castelia for the purpose of "sending a message" to Team Plasma, killing Suicune in the process. Not to mention her deliberate Kick the Dog moments against Kyle following him destroying one of her bombs.
Adams either crossed it when she set Leviathan loose on Goldenrod, or when she butchered Team Magma.
McKinley made a point of effectively blackmailing Sonja and Ray into becoming the Sixth and Seventh Children, respectively, in addition to kidnapping and doing something to Levi in order to make him the Eighth.
Rescued from the Scrappy Heap: While still not particularly well-liked, Silvermind has at least improved in terms of (for the most part) no longer being seen as purely a plot device for the Manaphy Arc. While her attitude and actions toward Kyle and Esen earn her Jerkass points, they are at least mitigated by the fact that they are in line with her established personality.
For some players, Kyle became a huge drag to read for some time due to the sheer amount of horrors that happened to him and his subsequent angst. Thankfully, his emotional and mental recovery has helped him recover in a meta sense, as well.
Saved by the Fans: Hayes was originally intended to remain comatose until the culmination of Ford's plan. Requests to see more of her resulted in her being brought back for one more mini-arc.
Carl Sandrock, of Manaphy Arc infamy, and Soil Colossus, Inc. by extension.
Dan the Mad, for being an annoying troll with no actual value in the story aside from forced comic relief.
Samuel Freeman for similar reasons to Dan the Mad.
Silvermind, for the longest time, due to her Damsel in Distress nature stemming from being created as a plot device for the infamous Manaphy Arc. Lessened somewhat as of late by her becoming more involved in current events—most notably those in Cianwood City.
One would be hard-pressed to find a fan of Gerald Hikari.
Travis, Zoe's school bully, is disliked to the point of being jokingly nicknamed "Travis Tea." This extends to her other classmates, as well, but Travis in particular is just a bad kid.
Both Ace and Bluefalcon. Two highly-ranked female members of their respective teams with pre-established facts and actions that could have led to some very interesting character development, both killed off rather lack-lusterly early on in the story. Parugi himself cites the early deaths of these two (particularly the latter) as deep regrets.
In general, this is a particular bane of the RPG stemming from occurrences at the beginning of its story. Players had a tendency to join, request and propose the introduction of their own organizations or other important characters, and then drop out of the game before doing anything of note with them. As a result, they become extraneous additions that must be dealt with and removed, often to mixed opinions, as they otherwise clutter the game's story. This can be seen in cases like Soil Colossus and Team Energon, both original groups, and Team Magma, led by Maxie and thus an immigrant from Pokémon canon.
Some sentiments about this have been shared regarding characters like Ash Ketchum, Maxie, Mars, Saturn, and other official-series characters. At the same time, some of these suffered from the above fate—having been abandoned by players who otherwise had had plans for them—while others were never supposed to be a main focus of the story to begin with.
Again, the Manaphy Arc is the one that immediately comes to mind, for good reason. Despite the amount of investment that was put into it, poor execution on the part of its managing player resulted in virtually no payoff and much backlash from the players involved.