I sorta skimmed this guide randomly so I'll give me two cents as I read it:

Veigar is a counter to most AP Casters/Carries in the LATE game. This is coming from a heavy Veigar player, might I add.

His early game is a joke, you need to bully him to stop him from farming his Q. If you stay away no matter what and let him farm his Q all the long, he'll insta-kill you whether you like it or not.

No mention of Talon or Zed? Assassins with extremely high mobility that can eat Vel'Koz up quicker than Veigar or Ryze could hope to do?

First spell should be either Plasma Fission or Void Rift. You do not leave one or the other for level 3. Tectonic Disruption isn't prominent enough in the early game, won't help you farm as quick as Void Rift and won't harass as well as Plasma Fission. It's mainly used as a disengage or to set off the last mark of your passive, which you can do with just Plasma Fission and Void Rift since Void Rift procs twice.

Boots of Swiftness is pretty situational, if they have tons of CC but even then Mercury's Treads are way better, otherwise just build Sorcerer's Shoes. Boots of Swiftness are really bad and not even a Hecarim player would build them if he was smart.

First back should be getting you Chalice of Harmony not Fiendish Codex. You have early game mana problems as Vel'Koz since he needs to farm quickly as well as harass his lane opponent so they don't exploit his horrible mobility.

Your item set is extremely unclear , really. Without any hint as to any of the reasons why we should pick those.

Also no Rylai's Crystal Scepter? Maybe paired with Liandry's Torment? Or even just Rylai's Crystal Scepter alone. The slow on all your spells will help tons in escaping, especially since Void Rift has no casting time so you can use it while running, slowing enemies behind you.

The guide has no coding, lots of incorrect names and typo's, and needs a ton of more work.

Also, another tip: It's called Organic Deconstruction. Not destruction. Just sayin'.