...or in an even more cynical view, let's big corporations and trolls to file patents for things that have long been in use but nobody even thought about patenting.

That's not how it works. It doesn't allow you to patent prior things because you're first, it is just to kill of disputes when people patent something "simultaneously".

Considering the patents that have been granted, I'm not so sure about that. Maybe it's supposed to be like that in theory, but in practice it seems companies can copyright basic shapes and colors.

It's not and never has been that simple. Apple didn't patent the square with rounded circle - they panted the square with a rounded circle in combination with a single button at the bottom and with a specific UI in the middle laid out in a specific way with specific features.