Frankly his main gripe is that JS = FP, CoffeeScript = OO.
The 3 gripes you point out are mostly a consequence of Coffee choosing to do OO instead of FP & then needing hooks into JS's world to achieve this end. From the article - "CoffeeScript sees the world through OO’s eyes. When I see JavaScript, I find beauty in it’s ability to be a dynamically typed Functional programming language."
His example is known by various other names, most commonly http://www.google.com/search?q=lots+of+little+objects
He wants just 2 "objects" ( he more specifically wants unstructured objects, or plain structs ) - sammy the python & tommy the horse. Functional JS gives him just those 2. But OO CoffeeScript gives you 5, or even 6 if you count hasProp.( var Animal, Horse, Snake, sam, tom, __hasProp. )
The more dramatic way to document this behavior is to have say 100 cats & 500 rats, whoe identity is captured in an int. With FP you'll be able to happily get away with just 2 "objects" - 1 cat and 1 rat ! The int indexing will happen via a function call. With OO you will have 600 little objects plus a bunch more for the classes and the hasProp !!
Here's another one I've seen - If you get two programmers to write a paddleball - one in functional JS, and the other using Coffee OO. The Coffee one will lag pretty soon. The Coffee guy will have a Ball object & a Brick object & a Wall object & each gesture will get captured as an object as well. So when the player moves the arrow keys to move the paddle, each move's x,y coordinates will become a gesture object & then gestures are passed to the ball & the wall to determine collisions....soon you'll have 1000s of gestures & the pgm will slow down unpredictably as the gc kicks in.
The functional JS guy won't create a single gesture object, he'll simply call some collision detection function directly with the x & y, so you'll see much better performance.
Ofcourse the coffee OO code will look a lot prettier than the FP one littered with curlies & function calls, but like the author says, "JavaScript’s function keyword and curly brackets aren’t ugly to me, they are useful indicators of code smells."
So pick your poison.