I suggested this a while ago but I feel it's time to re state it, the fix for veigar is simple, it isn't an issue for him to be a slighlty niche charater, a mage hunting mage is cool. The issue really is two fold, Firstly, almost all of his abilities have a commonly produced counter, secondly he is prettymuch the only hero to have an ult that is inheirently worse against a % of heroes. This is annoying as an ultimate is supposed to be your big game breaker, and when it's extremely common for non mana heroes to be at least 1/5 of the other team, your gamebreaker becomes marginalized very quickly.
My proposed fix would to be to turn his ultimate into his Q skill, reduce the damage, but keep the scales with mana property and gives AP with kills. This new ability would be your bread and butter skill, it keeps your magehunter properties intact and keeps that core premise of the slowly growing mage intact while giving you a strong ability that isn't the cornerstone of your hero.
My idea for the replacement ult would be an all or nothing nuke that used 100% of your current remaining mana for a huge nuke that would be proportionate to the ammount spent. This would add much needed finishing power and be a fun mechanic to seperate the good from the bad, it's going to hurt, but once it's used you're prettymuch food.