Even making relationship features purely optional changes the mechanic, focus, and feel of the game. That's simply not what Pokemon is.
I'd argue that making the protagonists older ,making the Evil Team want to liberate Pokemon from humans, and adding a guy like N who believes that pokemon and humans should be separate already changes the feel of the game. If it's optional it doesn't change the focus, the focus is still on the main plot.
And can you really say what Pokemon is and isn't? I'm fairly certain that's up to Gamefreak to decide, not us.