>>54567846And the MC of PLA, and DPPlt/BDSP also catches Giratina, and Darkrai which are generally regarded as "evil" pokemon, same with any game with lore around those pokemon actually like gen V as well.
Also the gen 2 HGSS iirc, after defeating Giovanni its implied he kills himself right after, though that did get retconned but still.
Oh, and Gen V part 1, you know, the events of the story leads to team plasma pulling a 9/11 as part of the plot of BW2 (but with ice).
Not to mention all the times you catch pokemon that the locals might depend on for one reason or the other and you just whisk them away to HOME or whatever, like in the last gen's DLC and that dumb deer legendary, what's going to happen to all those old people with their lands becoming a frozen shithole while you whisk away the King of Bountiful Harvest to HOME?
Or any legendary for that matter, least of all one's like the creation trio/arceus.
It goes on and on. The protags of the games usually aren't exactly the "good" guys when held up to scrutiny, but then GF isn't exactly good at writing.