Personally, I don't think "unique-ness" is valuable in and of itself unless it creates unique play.
The target AP ratio on Veigar's ult doesn't create interesting new play or counterplay opportunities for veigar or his opponents. If you're playing Veigar, you have no control over what your opponent buys. If you're playing against Veigar as an AP carry, it's not as if you can "counterplay" him by refusing to build AP.
It barely influences the way Veigar plays, if at all. It's a minor incentive to target enemy casters, rather than ADs, but he should have more than enough burst to 100-0% a marksman or squishy AD assassin by late game.
His ult is a pretty boring skill. The target AP ratio doesn't make it any less boring. It just adds damage. I'm inclined to agree with OP. His R is "unique" but not in an interesting way. If Riot decides to nerf Veigar, this seems like a fine place to do it. Like I mentioned above, it's not like Veigar even needs the additional burst to 100-0% enemy casters late game.