I always interpreted them "stopping" the Pokemon in question as being down to their quelling the actual rage emotion and breaking the Red Chain, rather than being powerful enough to actively undo or battle the mascot in question. The reason Giratina has to intervene in Platinum then came down to them only being able to stop one "in time," with Giratina showing up due to the continued distortion messing with its realm, at which point it steals Cyrus, Palkia/Dialga have no command anymore, and just go away after maybe the Lake Trio finishes up with both chains.
Legends Arceus presents the scenario working in the opposite direction, with the Red Chain being used to quell a rampaging Palkia/Dialga but the Lake Trio themselves not intervening when the other appears. It might be they can't match one of them at all, their influence literally just being to remove the Chain from the equation when it's the cause of the problem instead of the solution.
Kantonian Farfetch’d, as a “joke” Pokémon, have been hunted because of their juicy meat, as well as their luxually delicious leek they carry with them. The species were generally too weak to fight back against predators, thus their number dwindle over time.
One argue that Ditto can compete well in the ecosystem, but the confusion they can cause will end up backfiring on Ditto. Transform and Imposter can be a double-edged sword for Ditto in the fauna.
Similar issues with Farfetch’d, except replace Leek with Present.
It can go on and paint scary thing that could at the very least stuns potential predators, but without any real strength to fight back, once ambushed or surrounded, the Smeargle is good as dead.
The Porygon line, while manmade, can escape to cyberspace from mugglers to predators alike. Castform doesn’t have that perk obviously, and their stats aren’t even good enough to make the most of it’s Ability, which means that any predator that relies on brute force will quickly take down Castform.
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The two firefly Pokémon runs into a problem of “master of none“ syndrome, and Illumise tend to be too independant despite their lack of specialty other than their aroma, while Volbeat tend to be too distracted by Illumise’s aroma. As a result, are easy pray for quick, swift predators, among them being bird Pokémon like Talonflame and frog Pokémon like Greninja.
Not exactly “stupidly rare”, but their blind obsession of love and mating, they leave themselves wide-open to predators like Sharpedo.
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I included them as “stupidly rare but also weak” Pokémon considering the good-in-theory, awful-in-practice luck-based Honey Tree that encourages save scumming more than most other situations. Due to their lack of capacity of battling, and Cherrim’s gimmick, Flower Gift, leave it even more open to physically-inclined predators and especially Fire-type predators.
Their big icy head scares off potential symbiotic allies, and specially-inclined predators can easily bypass it’s Ice Face. Eiscue can only hope to run away, but if cornered, they are toast.
Trying too hard to mimic the famous Stonhenge only leaves Stonjourner with effectively no Ability if lonesome, and still crippingly weak against Special Attacking moves. Pokémon that would eat the minerals found within Stonjourner will just use a multi-targeting Special move, especially Surf, to kill them swiftly.