(Warning: Major "Pokemon Fan don't find patterns" challenge failure ahead)
I don't know if this is unpopular as in disagreeable or just not widely thought of/held, but I would argue that divorced from what was done in later arcs with the characters (i.e. Lance coming back reformed for GSC and HGSS, or reveals with Yellow in the FRLG arcs), the Yellow Arc might be the "darkest" early Pokemon Special got while the Pokemon as a concept remained important to its story (see the above criticism of stuff like XY and SM arcs).
My basis here does involve the human characters in how the Elite Four are handled as antagonists: compared to organizations like Team Rocket, Magma, etc. the Kanto populace or at least big wigs are aware of the Elite Four existing but also regard them as too strong to act against without some serious prep and help. No one thinks it bizarre that one of them could beat a Champion as accomplished as Red was shown to be, even if contextually there's more at work there, and despite an obvious hatred/problem with them from the RBG arc the former Rocket Leaders (i.e. actual no-dressing-down Terrorists and Crime Bosses) and the protags arriving clearly consider working together necessary to challenge them. Maybe it's hindsight with real life molding my perspective but something seems eerily heavy and concerning about a villainous body everyone is aware of but also feels incapable of challenging bar a forced hand/Godzilla threshold.
Agatha is pretty unrepentant in essentially wiping out humanity as their goal goes, and given the flashbacks we see of a younger Lance and Lorelei, it almost gives me this impression that she fed into or conditioned their grudges to reach the point of intensity they display in that arc. Agatha is also shown getting away in a much more dignified/less broken fashion than any member save Bruno, who was mind-controlled into their cause anyway at that point. While every member is willing to kill for their cause, Agatha in particular has the most "targetted" efforts against Blue, which makes her less-sound defeat a lot more infuriating.
The big thing this makes me think of though is Yellow's final battle against Lance. Yellow spends a lot of the fight in her Martial Pacifist mode, defending herself but clearly hoping she can talk Lance down instead of having to fight him despite him clearly not sharing the sentiment. The fight itself almost feels like a perversion or dark take on Yellow's Empathic nature, with things like Blaine and Mewtwo able to challenge Lance if not for their link hurting the former to the point the latter stops fighting for his safety, or Giovanni displaying a brutal efficiency to match Lance in battle among the 3 Viridian trainers. A big moment on this front for me is when Yellow hears the thoughts of Lance's Dragonite, exhausted and injured to a near fatal degree but still only concerned with seeing Lance's goals through, which has two dark perspectives in Lance either ignoring or missing the state his own Pokemon is in because he's that single-minded in his plan by that point.
In the end the only way Yellow's able to stop Lance is to fight and defeat him head-on, something very contrary to how she wanted to live but that people like Blue told her wouldn't be enough against an enemy like this. Yellow outright cries at the prospect of her Pokemon evolving or changing, a process that in terms of character is very analogous to aging/maturing in the franchise as it has gone on (both with things like the anime arcs or Spin-offs like Mystery Dungeon treating your 1st-stage characters as Children). The climax of the battle requiring Yellow's team to evolve to go toe-to-toe with Lance and save everyone has a sort of "Loss of Innocence" air to it with that context, as the entire fight pushes in Yellow's face that her pacifist nature won't work and won't reach some people, only able to stop Lance by beating him down so he can't continue his plan. Compared to most arcs, while the story conflict is won, the protagonist's philosophy doesn't bear out and has to be defied if anything when pushed to the extreme. Even if Lance is less villainous in later appearances, this is less out of Yellow convincing him regardless of the fight than other matters on his mind like Lugia being controlled taking his attention (and HGSS suggests he's outright intimidated/afraid of/unbalanced by Yellow when Petrel disguises himself to get the drop on him).
I can't really think of another Pokemon plot or scenario that ends in a moral/personal failure, minor or otherwise, for the protagonist. Even with antagonists who can't be reasoned with/reformed like Ghetsis or Volo, the resolution still has them beaten because your method overcomes theirs rather than having to meet and beat them on their own level like this arc.
I don't know if this is unpopular as in disagreeable or just not widely thought of/held, but I would argue that divorced from what was done in later arcs with the characters (i.e. Lance coming back reformed for GSC and HGSS, or reveals with Yellow in the FRLG arcs), the Yellow Arc might be the "darkest" early Pokemon Special got while the Pokemon as a concept remained important to its story (see the above criticism of stuff like XY and SM arcs).
My basis here does involve the human characters in how the Elite Four are handled as antagonists: compared to organizations like Team Rocket, Magma, etc. the Kanto populace or at least big wigs are aware of the Elite Four existing but also regard them as too strong to act against without some serious prep and help. No one thinks it bizarre that one of them could beat a Champion as accomplished as Red was shown to be, even if contextually there's more at work there, and despite an obvious hatred/problem with them from the RBG arc the former Rocket Leaders (i.e. actual no-dressing-down Terrorists and Crime Bosses) and the protags arriving clearly consider working together necessary to challenge them. Maybe it's hindsight with real life molding my perspective but something seems eerily heavy and concerning about a villainous body everyone is aware of but also feels incapable of challenging bar a forced hand/Godzilla threshold.
Agatha is pretty unrepentant in essentially wiping out humanity as their goal goes, and given the flashbacks we see of a younger Lance and Lorelei, it almost gives me this impression that she fed into or conditioned their grudges to reach the point of intensity they display in that arc. Agatha is also shown getting away in a much more dignified/less broken fashion than any member save Bruno, who was mind-controlled into their cause anyway at that point. While every member is willing to kill for their cause, Agatha in particular has the most "targetted" efforts against Blue, which makes her less-sound defeat a lot more infuriating.
The big thing this makes me think of though is Yellow's final battle against Lance. Yellow spends a lot of the fight in her Martial Pacifist mode, defending herself but clearly hoping she can talk Lance down instead of having to fight him despite him clearly not sharing the sentiment. The fight itself almost feels like a perversion or dark take on Yellow's Empathic nature, with things like Blaine and Mewtwo able to challenge Lance if not for their link hurting the former to the point the latter stops fighting for his safety, or Giovanni displaying a brutal efficiency to match Lance in battle among the 3 Viridian trainers. A big moment on this front for me is when Yellow hears the thoughts of Lance's Dragonite, exhausted and injured to a near fatal degree but still only concerned with seeing Lance's goals through, which has two dark perspectives in Lance either ignoring or missing the state his own Pokemon is in because he's that single-minded in his plan by that point.
In the end the only way Yellow's able to stop Lance is to fight and defeat him head-on, something very contrary to how she wanted to live but that people like Blue told her wouldn't be enough against an enemy like this. Yellow outright cries at the prospect of her Pokemon evolving or changing, a process that in terms of character is very analogous to aging/maturing in the franchise as it has gone on (both with things like the anime arcs or Spin-offs like Mystery Dungeon treating your 1st-stage characters as Children). The climax of the battle requiring Yellow's team to evolve to go toe-to-toe with Lance and save everyone has a sort of "Loss of Innocence" air to it with that context, as the entire fight pushes in Yellow's face that her pacifist nature won't work and won't reach some people, only able to stop Lance by beating him down so he can't continue his plan. Compared to most arcs, while the story conflict is won, the protagonist's philosophy doesn't bear out and has to be defied if anything when pushed to the extreme. Even if Lance is less villainous in later appearances, this is less out of Yellow convincing him regardless of the fight than other matters on his mind like Lugia being controlled taking his attention (and HGSS suggests he's outright intimidated/afraid of/unbalanced by Yellow when Petrel disguises himself to get the drop on him).
I can't really think of another Pokemon plot or scenario that ends in a moral/personal failure, minor or otherwise, for the protagonist. Even with antagonists who can't be reasoned with/reformed like Ghetsis or Volo, the resolution still has them beaten because your method overcomes theirs rather than having to meet and beat them on their own level like this arc.
