When it comes to configuration, I think we need a mix of both CLI, and GUI.
Take an Exchange server for example: Everything is doable from the CLI, but it is tedious and noisy, especially for listing stuff, or searching objects.
That is where the GUI takes over, which lets you unfold the mailboxes, sort contacts or changes indivudual properties (and it is actually easier to do from the GUI, trust me!)
Now evereything in the GUI is bound to a command, which can be run in the CLI. The GUI gives you acces to predefined commands, so they complement each others pretty well!

From a desktop point of view, it is also easier to use a graphical interface rather than text only. The fact the TTY week is a difficult challenge is sufficient to prove it!
For a good experience, all GUI applications should be able to communicate with each others (hint: system clipboard!), to provide a slick and smooth interface.

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To sum up my idea, we need both CLI and GUI, as they complement each other well, and both solve different cases.
When it comes to the IPC, I am confident that textual interface is a good way to go, over binary blobs. Parsing text is mastered today, so it's cheap to implement. It is also human readable, and less subject to data corruption.