I've actually read multi-page threads about the nature of the infinite plans and it made my eyes bleed. I shall never go down that road again.
Excepting that this is the internet and all the weirdness that entails, I am curious as to how and why this is the case. I mean, the infinity always seemed pretty straightforward "you travel at the speed of plot"-ness to me. In PS it was given some more specific treatments and ramifications, but everything was given that in PS.

As a general nature, why did it boggle you?
It is entirely possible that I am just totally ignorant as to how or why that may be a problem (or how changing "infinite" to "finite, but for all intents and purposes still containing anything and everything you want" fixes it).
As for your second complaint, well, I see your point and if it makes any difference, I think that I read somewhere that the 4e MotP does give some guidance to DMs in creating their own cosmologies (isn't there where the Great Wheel part comes in?), but I also understand that WoTC is also in the business of selling books and they need to maximize their audience. Though they specifically mention monster origin and spell effects, they're biggest concern, given the reference to the FC series in relation to Eberron, seems to be how the fluff impacts sales. IMO, they're in a bind, as if they don't anchor planar content in at least some kind of fluff, they get flack, and if they do anchor it to fluff, it is less appealing to people who use specific settings that differs from the initial fluff. While I personally really like the World Axis cosmology based purely on the fluff, I can immediately see the benefit of a unified but extremely flexible cosmology (with the flexibility coming in through individualized Astral Domains, for instance).
It's a bind, but it's not a new one. It's the same puzzle that has faced every single edition before it, and it is that balancing act between being a game (with a specific, limited field) and being a system (broad enough to accommodate very different games).
It should be trivial for D&D to not hardwire the cosmology in. Heck, in a lot of ways, it's easier in 4e than it is in 3e. What does your campaign loose if you ditch the Shadowfell? You maybe change some origins on the fly and re-fluff a ritual or two if you need to, but most of the time, it won't even affect anything.
So what's the big deal? Why tell me I can't/I shouldn't/you won't? If it's
even easier in 4e, and 3e decided to do it (to much acclaim, no less!), the only other answer this article seems to give is a financial one: because at some point, we want to sell you a book about the Shadowfell, and if you don't use it (or if our published settings don't use it), that means that less people will buy it.
That answer
blows. Rather than a book on the shadowfell, give us a book about Realms of the Dead (including the shadowfell as the penultimate example, but giving us alternates and letting us see in your toolkit how you made it). Any book that is too narrow in focus to appeal to every group almost regardless of campaign setting style probably needs to have its focus broadened, anyway.
I don't mind the World Axis cosmology as a generic fantasy/D&D cosmology. It's fine for that. It works, it's good with Planescape, I'm content with it. But to pretend that it's appropriate for every setting is absurdly misguided, it robs DM's of one of the more enjoyable aspects of world-building, and the arguments against it don't hold up under scrutiny. It doesn't match the way people
actually play the game. It doesn't match the way the
world actually works! It robs vitality and variety from the game.
It's a bad idea in so many ways.
Its no dumber than forcing the Great Wheel on Athas or Krynn.
This I totally agree with. I think 3e's method of "multiple cosmologies" was an
awesome thing. It meant I could have my Great Wheel Olympus in Planescape and that some greek-inspired campaign setting could have a more authentic Olympus that worked better for it, and we'd all be happy about it. The bits on cosmology in the 3e
Deities and Demigods were awesome. The alternate cosmologies in the Manual of the Planes were awesome. They even had great traction! Eberron's dream world and the Orrey setup were very popular, and they came basically right from the 3e MotP!
I don't like shoehorning every cosmology into one. Forcing the Great Wheel on everything is as bad as forcing the Great Bobbin on everything.