Yeah, that "D&D is not D&D without the Great Wheel" line is kinda bad. It even seems to flatly go against the tone of "change the cosmology to match what you want!" tone they're trying to go for in the article. How did that kind of thing slip through an editor? Do they edit these articles?
In the same way that "D&D is not D&D without Elves, Drow and Orcs" line is kinda bad? It doesn't do away with "[you can] change the cosmology to match what you want!" or even you can change the races to match what you want. D&D needs a baseline, for many years the great wheel was that baseline. For many D&D isn't D&D without it. They build the great wheel and anyone or everyone can discount it and make their own thing, just like what they can do with elves, drow and orcs. That doesn't mean they shouldn't make elves, drow and orcs. It has nothing to do about putting down 4e or saying the 4e planes are bad, it is about realizing and addressing that not everyone was on board with the 4e design.
I certainly preferred the elemental chaos and astral sea over the excessively over-designed Great Wheel and Inner Planes, but I honestly would like to see something even more new. Or rather, I really would like to see them abandon the idea of a core planar cosmology entirely.
First, I'm glad you liked the elemental chaos and astral sea, I can understand you even liking it over the well defined great wheel (and inner planes). That doesn't mean that they can't keep it or a version of it. I took aspects of the 4e cosmology for my game and integrated them with a VERY 3e cosmology base. It works great.
Second, I would want to see them evolve and advance the core cosmology instead of abandoning it again in favour of something completely new. They tried tearing down the cosmology and rebuilding it with similar (almost identical) pieces in 4e and that didn't work for many. I would have rathered something completely new but it seems unlikely as they probably want to keep nine hells and infinite (or 666) abyss layers. So, again, evolve and advance not rewrite from scratch.
Third, I do like the idea of incorporating cosmology into the world. I think it works GREAT for a lot of mythical (real world myths) stories. Mount olympus is supposed to be in greece (iirc) afterall. A lot of what we would consider planar hopping is basically just them going to obscure or remote areas of the world. I think that a lot of these aspects DO NOT work in a lot of newer stories and certainly don't work well in games where you ARE going to be leaving your little plane behind.
Fourth, D&D has always had a history of mixing up their cosmologies as it is. Eberron and Faerun both had different cosmologies than the default greyhawk one, and different again from spelljammer. So I don't see why that is so hard. I think the flaw for any discussion about cosmologies comes up when you try to talk about them in a vacuum without knowing the core world that they relate to. For example, I've never had any use for the inner elemental planes but I know countless games which have used them to great effect. Hell a notable NPC in my game has a cubic gate which links directly to the elemental plane of water, but it has never really come up.
Take everything I've said with a grain of salt, I just wanted to give my thoughts on the subject.