Without more context, this feels like vaguebooking: it seems like it's aimed at a particular person or type of person, but it leaves me guessing at the target. Maybe that means it's me. I wish there were some examples so I knew what kind of clever the author had in mind.
Examples would help, but there's a clue in what he suggests as an alternative: "be polite and to the point". I think any type of cleverness that's indirect or could be perceived as impolite is the kind of cleverness he's talking about.
It probably has something to do with the on-going saga of his relationship with the "Sad Puppies" crowd, though I think the Sad Puppies didn't actually form until years later. And yeah, I wouldn't be surprised if it were an oblique response to something someone tweeted at him.
Getting more specific than that would probably require doing some Twitter archaeology, and I doubt that would be a particularly edifying enterprise. As entertainment options go, watching Scalzi get into minor spats with people who don't like leftist SF/F figures is right up there with reading YouTube comments.
Sometimes I make jokes that go over the recipient's head (almost never directed at them); it makes them feel a bit dumb and either makes me look like a jerk or poor at communicating.
I've tried to pay a lot more to context (what do I know about the person whom I'm talking to? what are their interests? what do they probably know about, and what not?), but it's still a work in progress.
In the meantime, most of my jokes, puns, or wit will get cut.
Yeah, I'm having a similar problem, I don't really understand what this is referring to. I can make guesses, but no way to know if I've hit the right thing.