But there were a few things about TNG that rubbed me the wrong way, and the biggest of those was the Prime Directive. I couldn't define why it bothered me back in 1990, but there was something very wrong about it it… something anti-human. Now, however, I understand, and perhaps you'd like to as well.

Let Me Count The Ways
Yes, that's a Shakespeare/Picard riff.

Here are five ways the Prime Directive was inherently flawed, four of them damaging and the fifth evil: 

#1: It was stupidizing.

The first problem with the Prime Directive was that it made the captains stupid. Rather than doing what they knew had to be done, they had to contend with a wrench thrown into their formerly strong minds. It was, to have fun with words, stupidizing to those captains. It made them delay rational choices. In the end they ignored the Prime Directive anyway – reason and decency demanded it – or else they found some clever way around it.

#2: It was a cheap plot device.

Writers for TV are urged to create conflict, and either exterior conflicts (Kilngons and Romulans) or crises of conscience will do. And so the Prime Directive became a fast, cheap way to give the captain a moral conflict. In the end, the captain would, again, either ignore the Prime Directive or find some slick way around it, because the audience would have been repulsed if he or she didn't. That's not good writing.

In some episodes of the later series' you can see the writers struggling for a plot that will make the Prime Directive look good. Those are among the least satisfying episodes of the franchise.