My theory on this is that GUI automation is way harder because most solutions requires the developer to explicitly spend more time on implementing something that is not usually useful to sales (non-automatable applications are the norm, and people don't decide to buy apps based on whether it supports automation or not).
CLIs are much easier because the primary interface (standard out) to communicate with the user is basically the automation API (whether it is stable or not). If you're a command line program, (unless you're doing something super wary), you're automatable.
My personal opinion is that the best way should support automating based on GUI interfaces… although I don't have any great ideas how to support various interfaces that are e.g. modal or contextual. The clipboard is basically poor man's pipes in the GUI world so we could take some ideas on how the clipboard and the source/destination application negotiate data types, and there probably are better ideas.