It is entirely possible for an ability to be overly powerful and not be an issue, only to become a problem after the champion is changed.
For precedent, look at Wither. It was an absurdly powerly, unfun, and really stupid skill, that no one coplained about because:
A) Nasus was rarely picked
B) Nasus was weak enough that having Wither wasn't enough to make him troublesome by itself.
Fast forward to after Nasus gets a series of small buffs that add up to make Nasus a formidable opponent. All of a sudden, people realize that an ability that amounts to a point and click 5s stun for auto-attack champions is kinda bullshit. Wither gets its AS reduction chopped in half.
Now, as I said, this is just my guess, but if Riot feels the need to cut power from Veigar's kit, I would wager the ult would be what takes a hit. It has all the features that Riot tends to despise:
A) Point and click ability with massive payoff
B) Low/no counterplay
C) A certain, non-obvious, burden of knowledge. (does damage based off your own AP as well, with no indication of this in-game)