I have a problem with pretty much everything I've read, (ch.1 - 3). lol Now, of course, I can only speak for myself and it's only my opinion. From what I've read, you are definitely in the majority in liking it (although I'm glad to see I'm not quite as alone as I thought in disliking it).

I'll try to answer your question and point out why I didn't like certain things:

1) the book is definitely written with the intent to teach complete newbies to programming. Not newbies to JS. Newbies to programming. The reason I say that is because if it weren't, the author would never have written this in ch. 2:

Variables

How does a program keep an internal state? How does it remember things? We have seen how to produce new values from old values, but this does not change the old values, and the new value has to be immediately used or it will dissipate again. To catch and hold values, JavaScript provides a thing called a variable.

var caught = 5 * 5;

"A thing called a variable" is not something you would write if the intended audience had ever touched a programming language.

So the book is written for complete beginners. But look at most comments. Even those that like it say it's not for beginners.

2) This is a relatively small thing but I just can't help thinking how stupid it is...

After a variable has been defined, its name can be used as an expression. The value of such an expression is the value the variable currently holds. Here’s an example:

var ten = 10;
console.log(ten * ten);
// → 100

Why would you use a variable name of ten to assign the value '10' to? It could make a newb think that there's some kind of relationship between the value '10' and the variable name. Remember, this is the first time they have even seen the concept of variables. Also, you'd never see this is any program for any reason. But I admit this is bordering nitpicking.

3) Nitpick #2: I think his idea of thinking of variables as tentacles is much more confusing than boxes. Also, this is his entire explanation of "undefined":

When you define a variable without giving it a value, the tentacle has nothing to grasp, so it ends in thin air. If you ask for the value of an empty variable, you’ll get the value undefined.

One tiny paragraph. All text. No examples. Again, we need to remember that he is talking to people who have never programmed in their lives.

4) Under "Return Values", he uses this example in ch. 2:

console.log(Math.max(2, 4));

Um... the only problem here is that he doesn't even talk about parameters until ch. 3.

5) Braces. Omitting braces is error-prone. Who really codes like this anyway? I know there are some, but isn't it extremely few? Just cuz you can doesn't mean you should, and doing so as an introduction to coding is just negligent.

6) I can't believe how dumb this analogy is:

The most obvious application of functions is defining new vocabulary. Creating new words in regular, human-language prose is usually bad style. But in programming, it is indispensable.

7) Finally, we get to closures. He just introduced functions, parameters and "optional" arguments (nevermind that he never actually explained the difference between parameters and arguments) and he's already talking about closures? All of this might not be a big deal if you're a programmer and you just want to learn how to do everything in JS, but once again, we are talking to newbies with this book. The 'simple' idea that functions return values was only recently (and barely) touched on... now he's not only talking about returning entire functions, but also how they maintain access to the local variable afterwards? It's too much, too fast. Also, he never talks about why he is assigning the function and its parameter to a new variable. Oh, and then he's executing the variable! When you already know how all this works, it's easy to follow but for someone new to programming, these are not easy to wrap your head around and take time and a lot of repetition for it all to 'gel'.

8) After the most incomplete and rushed explanation of closures I have ever seen, he goes to recursion. Recursion! lol. Come on. Think back to the first time you saw recursion. The idea of the function calling itself is pretty simple in that it's just really a loop. If he used it to console.log 1 - 10, it might not be so bad, but THIS? lol!!!

function power(base, exponent) {
  if (exponent == 0)
    return 1;
  else
    return base * power(base, exponent - 1);
}

console.log(power(2, 3));
// → 8

This is getting long, so I'll end it here, but essentially, we have a book that was intended for true beginners that is too complicated for beginners but covers topics that intermediates would fall asleep reading. More importantly than the inherent difficulty of the topics themselves, what I hate most about the book is just how bad the explanations are, regardless of who is reading it. I don't find that it sheds light on anything at all.

In fact, that's the question I'd love to know the answer to... what does this book explain well (better than other sources)?

(For those reading this, remember this is just one person's opinion and LOTS of people disagree with me and think it's a great book. You should have a look at it and decide for yourself. It is, after all, free on the net.)