Typed objects can make it harder to pipe commands together. How do you grep a tree when tree is an actual data structure and grep expects a list of items as input? You would need to have converters. Either specific converter between tree and list, or a generic one: tree->text->list.
>Something Windows does get right is the clipboard.
It useful, but the actual implementation is pretty bad. Opaque, prone to security issues, holds only single item, cannot be automated.