He's always been one of my favorites, when I was a kid I didn't really know what he was supposed to be and assumed he was just supposed to be a little patch of mold, they get a little "head" poking out of a "shell" if you leave em' alone for too long, but with the benefit of age, I think the little guy's supposed to be a nematode worm.
The shell is actually supposed to be like a stomach, this is why he learns gastro acid.
He's found in the ocean in Pal Park because most species of nematode are found in the sea. This is also why he's always shown on beaches in TCG artwork.
In the anime short film, the one with the Pichu Brothers in Big Town, he's shown switching heads from holes so fast it seems as-if there were an entire colony of Shuckle living in one shell. Like nematodes, living in a mass group.
I think that he's supposed to be an especially cute worm.