Only Game Freak knows the answer to that. However, I will try to explain the examples you have listed with logic!
Gulpin – Gulpin is fat and lazy, and therefore his eyes are shut. Same with Snorlax.
Cyndaquil – Cyndaquil is supposed to resemble a cute little mouse, so his eyes are done in a 'cute' fashion.
Skitty – Same as Cyndaquil, except she's a kitten.
Simipour – Doesn't he just look like the embodiment of happiness? Simipour/Panpour's eyes are closed because they are squeezing them shut out of sheer joy.
Brock – This has stumped literally everyone for years. Nobody knows that one.