except.... if that portion were removed then it would deal roughly 1600 damage. - your ~40% MR, or close to 1200 damage. for a single target nuke ability. (assuming rank 3 with ~~ 1000 AP)
in which case its still a projectile which can be outright negated by braum/yasuo, or dodged with zhonyas. and has a short range.
mind you, thats someones ultimate, of which hes a squishy AP mage who needs to get in deadly close to use it, making it highly risky for him to try.
or ya know, you could put a rumble ult down and chunk everyone in the team to half or less. as opposed to 1 shot a carry if you get close enough in that team setting. or same thing with a vel koz with dealing bonus true damage, (can deal upwards of 2k damage to MULTIPLE targets over the duration)
which is why its justified, because most other mid laners poke him or burst him before he gets that chance. very few get in close (sparing ahri, leblanc, fizz) and a bunch of others are tanky enough to tank it outright (malz, swain, brand, cho, galio, kassadin)
so who does it 1 shot? oh right, ADC's after the 35minute mark where he has amassed at least 300 bonus AP. but still doesn't doesn't 1 shot an ADC at that time. but hey, you dont need banshes, merc scim, guardian angel on your carry anyway.
now tell me, the largest, single target nuke ability in the game, shouldn't deal more damage.
why not just change the ability to deals X amount more damage when missing Y% amount of health? would that make you feel better? if it were used as an execute rather than a pick ability?
if you get close enough to veigar you deserve to take his R. if you didnt counter build and shut him down you deserve to get 1 shot if you are OUT OF POSITION, if the game isn't over at 40+ minutes