Almost all of these can be summed up as a "lack of player empathy." Bad game designers fail to understand that there's a line between "making a game that you like because it appeals honestly to your tastes," and "making a game that you like because you made it, and are willfully blind to flaws."
ZUN gets away with breaking any number of rules because, ultimately, he has a disturbingly strong sense of player empathy. Player empathy isn't making an easy game or a hand-holding one - it's figuring out what a player is likely to experience at a given point in play, given that they've never seen your game before, and adjusting accordingly. Even if his games are difficult, I was able to get into EoSD with poor reflexes and no real schmup background. Why? Because the "normal" difficulty level was well-designed, had a difficulty curve that was reasonably gentle up to the fourth level, and gave you copious bombs!
A bad designer would say, "Well, I'm making this for people like me, who are going for a Lunatic mode victory. I'll just make everything else tediously easy."
In some cases, though, the commentary misfires. I agree with the author that grind is a waste of time, but the MMORPG takeover seems to show that some people looooooove grinding. If you set up a strong reward cycle, with each successful acquisition unlocking new goodies and nifty designs, you can get people to grind like mad. And that isn't even starting on JRPGs.
Grinding isn't due to a lack of player empathy. It's the product of empathy with players who, on some level, like to grind. This is understandable - there's a weird obsessive addictiveness to it - but it's an astoundingly cynical device.
