I didn't like it in 2e, either.

The round hole of the One True Cosmology in that era did not fit so many of the square pegs that individual settings were.
How much did it really interfere with them though? Unless your world used a LOT of planar elements, it really rarely mattered. I ran Eberron without ever touching on the planes, and the planes directly affect the world itself!
If they're smart, they'll dodge that bullet in 5e, even with Defaultsylvania. I don't want the Orrey from Eberron kludged into the Great Wheel (for instance), I want it to stand on its own. If it's a light touch default that allows/encourages alternatives, that shouldn't be much of an issue if you approach it with open eyes -- you should be able to drop it whenever you aren't specifically working with it. Buuuuuuuuuuuuut, history shows a tendency for an e's defaults to filter into unwelcome places in the individual settings.
D&D is not Generic Fantasy; it can't (nor should it) handle fantasy from the Hobbit to Game of Thrones. Default assumptions will always filter through. You create a monster in the MM, give it stats and a pretty picture, and then the DM want's to know more. Where does it live? What does it do? Why is it in a dungeon guarding 120 silver pieces and a +1 sword? WotC has two choices: answer the question (and create a default assumption) or don't and tell the DM to "make it up" (which is hard, even for veteran writers to do).
Now, there is taking it too far: I don't want D&D to be tied to a specific pantheon (as 4e's deity feats were) for example. However, when you come up with a monster, you're going to have define a "default" so that the DM can accept or deviate from it. As long as the mechanics are strongly tied to it, that shouldn't be a problem.
Planescape didn't need Vecna.
Technically, he was only relevant when they decided to break Planescape. Otherwise, he was trapped on Oerth (where he belonged) or Ravenloft (where he didn't, but thankfully he was on an easily ignorable island, unlike Soth).
Dark Sun didn't need githyanki or eladrin.
Was there ever a reference to this? I recall in PS lore that Athas was "remote" and didn't have portals to the outer planes (just the elemental planes and stray portals to Sigil).
Eberron didn't need the World Axis.
Agreed here, but that's because Eberron specifically did a lot to be anti-Great Wheel when it came out, even breaking up the demons and devils across different planes. If it had used the default assumption to begin with, it never would have mattered.
FR didn't need "Returned Aebir."
Hey, that's nothing to do with planar crossover. Aside from being the worst way to fit in Dragonborn, that was pure Realms beginning to end.
Dragonlance doesn't need the Blood War.
Did Dragonlance even COVER a plane that wasn't the Abyss? Dragonlance worked just fine in the default assumption since it seemed the DM only cared about one plane anyway...
The Nentir Vale doesn't need the Great Wheel.
The default 4e cosmology is so damn close to the great wheel that I barely notice a difference.
None of these intrusions of the default make the settings themselves any better.
What intrusions? I don't recall the module where Dragonlance was overrun with baatezu and the tanar'ri chased them out, or when novel when the githyanki invaded Athas. Unless you had a DM who did a lot of plane-hopping and Spelljamming, it wasn't an issue. I ran my own setting for a long time and my PCs never ONCE cared to visit Faerun.
Which is really my big fear about 5e settings, and why I'm kind of a fundie about the negative default effects. I don't want 5e to do that thing that D&D tends to do.
D&D is built on them. To not be would be to make it GURPS.
Ignore the planes for a minute. Lets take the default D&D monster: orcs. Without a shred of "fluff" about origin or society, look at what we can tell about them:
* They're evil, often chaotically.
* They are strong and tough, but lack wits and smarts.
* They make good warriors and crummy casters.
* They can breed freely with humans and create hybrids.
* They tend to be horde creatures and are found in large numbers.
* They have the ability to use tools (weapons and such) but are very primitive otherwise (no heavy armors, no lands of their own).
Already right there, the default assumptions in their stat block rule out Warcraft-style orcs (which were not fully evil and are powerful shamans) and Tolkien orcs (which were corrupted elves and unable to breed without magic). So D&D creates its own mythology rather than just leaving it blank. Heck, by the planar logic they shouldn't be in the Monster Manual since neither Dragonlance nor Ravenloft even have them!
Lather, rinse repeat on everything form chromatic dragons to elemental-themed giants.
So three grumps. Could get down to one or two if they're good about handling the new settings. Could raise to six or so if they make the blunders that D&D has historically made and jammed Defaulsylvania's schnoz into every crevice or other settings.
Really, they have three options: defined world (akin to World of Darkness), tool-kit/generic (GURPS) or world lightly seasoned (D&D for most editions). I hope they keep the latter.