Personally I dislike that the ult is extremely situational and borderline useless against some champions until you've stacked up so much AP that your Dark Matter does more anyway. In the end it works wonderfully, I just find that it's hardly worth using until then. I guess you can argue he's a late game champion though, so whatever.
A more genuine problem I have with the ability is that, for the Tiny Master of Evil, it's an extremely lackluster ability. A single target nuke with a hardly noticeable animation with an effect identical to his smaller, non-ult ability (5 AP for a champion kill)? Honestly thank god it hits like a truck on some champs because the only satisfaction I get from this ability is watching their health bar disappear. You look at someone like Karthas or Fiddlesticks and you see ults that are appropriately devastating when used in the right situations. They can wipe out entire teams. The best Veigar can pull off with his ult is a quick single target kill.
Again, I'm not saying his ult isn't powerful enough endgame, I'm just saying it's kinda, well, dull.