The court objected to “an unnamed class of felons” being pardoned because that was apparently the best argument offered. Pardoning them individually seems to cover that objection.
It does not address the issue that the Virginia legislature passed a law, which was presumably signed by the governor at that time, which prohibits the restoration of voting rights for felons.
Unnamed, or through a process of pretending to be named, does not address the fact that this is a deliberate attempt by the governor to nullify that law without going through the proper legal process for doing so.
In any case, Republicans need to throw up every possible legal obstacle to prevent this obvious and deliberate attempt to stack the electorate for Hillary using the excuse of alleged "civil rights".