Doesn't bother me, since I generally like the Great Wheel to begin with, and use it with a few additions. It's the familiar D&D cosmology that been around since 1e, with a few extra details here and there. Only don't really care for the whole approach with the Shadowfell and Feywild bits. I'd rather a classic plane of shadow, and I generally view a fey plane as a connection between the Material and Outer planes.
As for connecting the other worlds together: The Great Wheel is likely the original cosmology behind Greyhawk, so I can't understand the arguments against putting it there. Similarly, it was long the cosmology behing FR as well. Mystara being more or less vanilla like the other two settings would probably use it too, but I'm not familiar with the setting's planar setups from B/X, BECMI, and RC (anything AD&D likely would have retconned it into 2e assumptions, so I'm not counting that material). That leaves the other worlds.
Dragonlance kind of fits poorly into the planar structure, so it should probably have a custom cosmology, no matter how much both Spelljammer and Planescape tried to shoehorn it in. Dark Sun, Spelljammer, and Ravenloft (with the exception of Ravenloft's initial 1e modules) were all first published as full setting at around the same time, the early 90's, and my guess is that they were all written to be in the Great Wheel. Planescape is just an expansion of the Great Wheel cosmology, so of course it should use it. Then there's Birthright which again was assumed to be Great Wheel (certainly Planescape made a few references to the setting which said as such), but any 5e reimagining doesn't really need to use the great Wheel, I don't think the planes were important to that setting. Eberron has its own assumptions, so should have its own csmolog. Don't really care about Nentir Vale myself, but it should probably stick with a cosmology closer to 4e.
Mearls should take the 3e MotP as a guideline here. Have the Great Wheel as the default D&D cosmology, but give the DM flexibility to make whatever arrangement he wants.