Okay, so you look at them, and what is the biggest difference between them and Hocotatians?
That's right, those eyes. Compared to most vertebrate eyes, they are very unique, which is why I decided to cover them first. No irises yet they can still dilate and constrict, seem to be completely immovable and rather large. What could be the purpose of such kooky peepers?
As we discussed, they appear to have no irises. However, they would have to have irises, as they can still dilate and constrict, and in most animals the irises do that. As for examples of their eyes doing that? Take this comedic image of Alph.
As you can see, compared to the images above, Alph's eyes are constricted, presumably from shock after scrolling on r/pikmin for a nanosecond.
Now, if Koppaites can constrict their eyes without irises... How? Actually, the white of their eye is not their sclera. THAT'S the iris. I believe their eyes are structured more similarly to that of dogs than humans, very large irises with normally non-visible sclerae.
If you watch some cutscenes and pay enough attention, you may be able to see that they don't move their eyes, rather they tilt their head around in order to look around. Hocotatians can indeed move their eyes, as you can see from Louie freakishly glancing around in the Pikmin 2 intro cinematic.
If you look at them in the above images, their eyes bulge out which leads me to believe they indeed have eyeballs instead of eye tubes like owls, an example of animal with mostly immovable eyes. However, owls can move their eyes at least a little bit, while Koppaites cannot at all.
As a result, I believe their eyes are just stuck in their skulls via being incredibly large, ocular muscles being vestigial from disuse. Alph's eyelids are not obvious due to the fact Alph keeps his eyes wide open thus his eyelids tucked behind his eye, the same applying for Brittany, while Charlie's eyelids do not due to his eyes not bulging as much as the rest of the gang.
However, there is an aspect that makes them even more freaky with their peepers.
This one makes them seem even more messed up... You see, their eyes, uhhh...
Is their pupil actually through their whole eye and the iris is more a covering that can push back, thus creating this? Very, very weird, as you can tell from these images. I saw a similar situation with the Bloons monkeys, but at least that's a more cartoony artstyle. Pikmin 3 being the least cartoonishly stylised game in the series, this certainly has freaky implications.
RANDOM BONUS I FORGOT BEFORE OOPS
During the Voyage Logs, Alph and Charlie's eyes kind of light up through the window. The reason why is that their irises are reflective, the light bouncing off of them strongly, possibly to keep tabs on each other's positions in the dark.
Anyways, I hope you enjoyed my first real biology post here on this blog, it was a real blast to analyse ingame footage to find all I can, speculate about the different aspects of them and put this post together!