I have a variety of mixed feelings reading this article and the comments, (Just letting you know.) The way the article struck me though didn't really tell me, "Your games are trying to FOOL you," rather, he was saying "here are some interesting tricks that developers can make a game more exciting," and "Really sucks when you know though, don't you?" That said though, it feels like it was trying to suggest that this was a one way street. The only way we'd feel like we'd have interactivity and fun at the same time, was to take away the interactive part.
But that's not the only way to have fun. As clearly demonstrated by all these posts, we all have different opinions and interests. Some people are simply sent over the edge by quick-time events, screaming at the horrid nature of pulling the wool over our eyes, essentially fooling us to have fun, while others might say, "Oh, so that's how it works, neat."
That said then, we can still like a narrative for different reasons. Some people simply like what happens and feeling of being drawn in, ala the examples of Half Life and Metal Gear. However, that said, games like Fallout 3 and Mass Effect, Although I liked the story, I most enjoyed just -talking- to the characters. Is it -the- most interactive thing? Not quite, but different things did happen based on our choice. Real choices. Narratives may not always be aided by interactivity, but that's not to say it can't be.
If difficulty is the real question, where we want everyone to be able to have the same experience, I think that's where difficulty settings come to mind. If you're just really good and want more of a challenge, you can play on hard. If hard is simply, well, too hard, they can play on easy, so everyone still gets to go through the story, and can have their skills really tested, without running the risk of players accidentally opening the curtains to realize what you did to "make" them have fun.