Virginia state law prohibits felons from voting.
The Virginia Supreme Court noted that if the governor issues an exemption for felons as a class, he has in effect abrogated a valid law.
Exempting each felon individually does not change the effect of what McAuliffe is doing, which is to nullify a valid law.
It would be like if a governor disagreed with a valid law banning heroin, and so he pardoned everyone convicted of selling heroin. That is functionally equivalent to nullifying the law, which the governor may not do.
“Functional equivalent” as alleged here may or may not be viewed by courts as a basis of action. It may be that the political process, or an even more specific legislative process specifying what due diligence must be, is the only way to oust such a governor or prevent his actions.