In the 1980s I took the Great Wheel cosmology, massively simplified it, and have used it (with some evolution that adds to, but did not really change, the basic premise) ever since. I have been so glad I did so ... keeping it simple has proven very helpful. If I find some new and interesting material, I figure out how to add it to the existing framework ... I do not try to rewrite the framework to incorporate it. I shoot for addition, not revision.
Putting that aside - if I were to work for WotC and be tasked with incorporating the M:tG planes into D&D, I would do so by keeping the unincorporated for the most part. They would live outside the Great Wheel, and they'd follow their own rules - but they would be accessible via planeshift and similar magics, as well as having the Great Wheel accessible via Planeswalking Magics. I'd also include rules on why we have rarely seen people travel between the M:tG and D&D Great Wheel cosmologies. If I were writing it, it might be that the connection between the two is the Far Realm, and that you must pass through it to get to the other cosmology, and doing so runs the risk that something will attack you en route, or hop along for the ride and infest wherever you arrive.
I'd write a M:tG PHB that had a few Planeswalker classes (or subclasses of existing classes), as well as basic M:tG cosmology, spells, etc... Essentially the equivalent of the current PHB without PART 2 (Chapters 7 to 9) and expanding the Appendix materials to full chapters, with a half page write up on each of the M:tG Planes that have been established.
Then I'd write books for M:tG planes setting books that included a chapter on the cosmology of that setting. Not for every plane - but for the ones that would be of most interest.