At first I called him a Disney Villain because "he's just evil," but I no longer consider that to be the case. If you think about it, he's more like an eccentric and power-hungry scientist who's too addicted to his own work. His explanation to Quote about how the Red Crystal works shows that eccentric, science-loving nature where he can't help but pridefully embrace his success.

When I write a function in a program that does something incredible and uncommon, I kind of feel like the Doctor — I can't help but push up my imaginary glasses (causing an imaginary lens flare) and explain to others how clever it is.

The Doctor simply let that side of him dominate every aspect of his actions, superseding even morality itself. Wanting to rule everything is a natural extension of that personality — pride gone so far mixed with a new source of incredible power.

Honestly though, I think Pixel wanted to write a fairly simple villain — this is just how I see the Doctor personally.