Veigar's Ultimate Balance!
will have more AP in most match ups. Why not reward him for playing well and scale this ability from differential in AP rather than a percentage of the opponents.
so something like
If Veigars total AP is more than 20% of the targets total AP above the targets AP then Primordial Burst will deal 25% additional damage.
Numbers: If Veigar has at least 121 ap when his opponent has 100 then his ult does bonus damage.
If the target does not have at least 20% of veigar's AP then he considers them to have a small intellect and doesn't use his dark powers for additional damage.
Edit: This is to address the fact that you are punished for building AP vs Veigar and the numbers could be adjusted so he can still delete you with an R press. Just to do so he will have to stack his Q effectively.