What you are describing is not the solution, it is the problem.
Many large-scale open source projects have found elegant solutions to similar problems. They let several APIs coexist for reasonable timeframes, phasing out unneeded ones and forcing people to migrate to new APIs after 1 or 2 years. I fail to see in what way the kernel would need to be different.
Said otherwise, Im not asking for refactorings to wait for 3 years. Im asking that they wait 6 months and get done cleanly.