Sigh...I guess I'll just take it from the top...
What I can gather is that Cook wants to remove magic items from character advancement altogether, rewarding characters with better loot for tackling harder shit, and "re-injecting the magic back into magic". While I can get behind this mission statement you can already resolve the first two "issues" using current rules in 4th Edition thanks to inherent bonuses, and a DM being able to place whichever monsters and magic items that she wants. Nothing he is saying is exactly new or innovative, and like many others makes me wonder if he has even read about the game that he is writing articles about. There is however a problem with how he wants to solve this problem:
His example cites a 4th-level character packing a +3 sword, with the understanding that if a character is smart and/or lucky enough, that she could feasibly get one and be better off for it. Since generally campaigns--whether adventure paths or episodic--involve the DM planning stuff with a rough challenge level and treasure already in mind, this is something that I guess I could see happening in a non-structured sandbox game where the players could hear about monsters and explore them at their leisure, though it does carry some problems:
The first is that if I am running a campaign and the characters hear about a dungeon or something with monsters consistently higher than they are, and still try to tackle it that they are most likely going to die. Maybe not in the first encounter, and maybe not in the second, but once they start running out of resources (or run into a bout of bad luck) if I do not start pulling punches then I could easily be out a party, or forced to find some contrived way to keep them alive.
The second is that if they succeed, then I either have to find some way to try and balance the encounters so that the guy with the good loot is challenged without making it impossible for anyone else to contribute, or run things business as usual, making things much easier for her (basically 3rd Edition Syndrome all over again). Here is a fun fact: if you want to reward your characters with better items than their level would indicate without drastically altering game balance, you can always use the rarity and artifact rules, which yet again already exist.
As for the mystery of magic items, he claims that this was lost in later editions--ie, 3rd and 4th--both because magic items are "expected" and because players can buy whatever the hell they want (though the rarity system introduced last year prevents you from buying uncommon and rare items).
This is one of many arguments that detractors of 4th Edition have made in the past, and it makes me wonder what version of D&D they played before: ever since 2nd Edition at least, magic items and spells have always had clearly defined effects, which more often than not could be gleaned through a simple identify spell (though 4th Edition made it easier with an Arcana check). However as one forum-goer put it, there are plenty of examples from mythology of clear-cut magic and magic items, so I am not sure they were ever very mysterious.
In a nutshell, everything that Cook proposes can be handled using the rules you already own, and if this was not disappointing enough he wraps up things with a very black and white poll: why does it have to be something that is decided by either the DM or the player? It does not. There is nothing wrong with players being able to buy some things and craft others, while still leaving the DM with some control.