Well aoe non-ult stun/knock up usually have some draw back. Like J4 EQ uses 2 skills and you see the flag first, and he has to go in. Yasuo need to charge his stun and has a relatively short window to hit it.
Its hard to compare Veigar stun with anything else since its pretty unique, but I think the closest one we have is Cho'gath's Q which hit the entire area but is smaller and its a knock up instead of stun. In this case, it also have a cast animation and a delay on the activation.
Veigar stun is basically unreactable before the change. This is especially true if the Veigar player knows what he is doing since its instant. The E nerf probably has a lot to do with the utility of it in the support role. Sure you can kill the little guy, but are you really willing to spent resources such as ult and summoners just to kill a support? If you do their carries will just clean up the rest of the fight. But if you don't dive and kill Veigar, he just stun your team over and over again for his team to poke you down.
And support veigar can afford to play a bit more aggressive and walk up for the stun compare to mid veigar. Since he is not carrying the damage of the team, its ok for him to get a good stun and die from the counter cc/ults/damage in addition to the reason I just mentioned.
So as much as I like little Veigar, his E needed to be change no matter what. But does he need some compensation somewhere else for being so squishy? Probably? Not sure on this one.