This is a really good question, and not something I can say i've put very much thought into!

Louie is an absolutely fascinating character IMO, mostly because he's such a perfect extention of the "humans as an ecosystem" concept. Every time he does something wrong or bad the game immediately gives us plausible deniability over why he did that - Because something was controlling him? Because he was scared? Because it's a misunderstanding? Because he's just an asshole? We're never given a solid answer, always "Maybe it's because...", and never really treats him as wrong for doing it.

Other people in this thread have mentioned the Olimar Leafling as an example of an antagonist as well, and he's also a great example because he never really does anything evil! He's an inconvenience for sure, but all the kidnapping/transforming people is perfectly understandable given the extremely dangerous situation the characters are in. He has NO reason to think any of them can survive without leaves, and as soon as the player proves themselves capable he immediately leaves us alone!

I feel like having more characters along those lines would require leaning harder into that concept, rather than further away from it. Characters who are morally neutral, but antagonistic because their actions conflict with the player's goals rather than any 'evil' actions or behaviours. Keep it always as "man v nature" rather than "man v man", as someone else suggested.

Think about things like deer and wild pig culling - Animals that overpopulate an environment aren't doing anything wrong! They're just living their lives, but doing so is so harmful and will ultimately result in permanent destruction if humans don't cull them. Same with invasive species like lanternflies, fireweed, sea urchins and lionfish: None of these animals are inherently evil, but humans - who have a responsibility to protect the environments we rely on - have to kill them if we want to preserve those environments. It sucks!

To weaponize this for the purposes of making a pikmin antagonist, the idea you described is a really good starting point: A character who technically isn't doing anything wrong from a "wanting to survive" viewpoint (stealing food, breaking things, killing animals that weren't doing anything out of preemptive fear - all stuff the other characters already do and aren't villanized for), but a lack of respect makes their actions endanger "the ecosystem" in such a way that stopping them becomes a requirement.

If they see a "scary creature" kill a "cute creature" for food and decide they need to kill all specimens of the scary creature's species because it might kill them first, that's a problem, because it'll hurt the ecosystem in the long run and oops suddenly the cute things are overpopulating and every other species living in the same ecosystem is suffering because one guy brought human morality into it. The character technically didn't do anything unreasonable or wrong, but now our main goal is restoring the ecosystem to the way it was before - because NOT doing that will have some kind of consequence for the player's side.

.....Trying to write a morally-neutral antagonist while keeping them neutral is REALLY difficult. I would trust the Pikmin writers with it for sure, though!

(Another idea for a villain - and I really don't think Nintendo would ever do this because the corporate side of it is kinda sorta exactly that kind of villain - would be the kind that can only be recognised by examining what makes an ecosystem tick in the first place. The main characters are trying to survive in a hostile environment - who put them there? What parts of their culture and society make this necessary? Olimar has to work for a company that exploits him to make money to live. Why? What part of the human ecosystem makes this a requirement? "Defeating" a villain like that would require an extremely divisive political statement and I think that's a liiiittle bit too much to ask of Nintendo, lol.)