Hmm, I missed this article first time through.
There's no such animal as an "intuitive" game interface. There just isn't. If developers are finding themselves slaves to cliche maybe they ought to consider actually *writing a tutorial* for once. And it doesn't have to be some pushy broad shouting at you over the radio seventy times to push the button, either. I mean, come on.
You're going to have a game where the attack button does different things based on direction and how long it's pressed? Okay then, design your tutorial level so that people HAVE to move back, forward, side-to-side, and do this for differing durations. End result? They'll accidentally do the many different moves enough times that they'll figure out what's causing it. They may even feel a little satisfied rush that they're "getting it". You can reinforce this by having little pop-ups or even achievements for discovering different moves. "FORWARD KICK!" "DOUBLE KICK!!" etc.
You're going to have a game where people can have different functionality by flipping items over? Give the character a nervous twitch where, when they're wielding an item that CAN be flipped, they periodically flip it around in their hand sometimes when they're "idle", so you get a random end when you go to use it. Not only will this educate the player in the fact that this flipping CAN be done, but they'll also get a nice visual cue on every item with this capability.
You want to get rid of the cliche'd crates and barrels? Mix it up a little. Maybe instead of the breakables exploding into a cloud of shrapnel when you wave the crowbar at them, your character instead executes a little timed "opening" animation. Let them use the crowbar on more things in the environment, too--maybe if they use it on an overhead wire, they can zip-line over to another part of the area. They can lever up grates/manhole covers/paving stones and look inside. They can smash electronics to disable gun turrets. They can temporarily use it to bridge electrical gaps and activate electronics. If you're using stuff in the environment enough, I bet you won't even notice if there's not anything around to smash.
The trouble comes when you present a game that seems to play in every other respect exactly like the cliche and expect people to pick up on the change. The entire game needs to change to reflect what you've done in some way. Maybe minor, maybe major, but you have to look at it as an integrated system.