Whether it was intentional or not, these villains were so well-received that they took a life of their own. That's not to say that their respective heroes are bad. But when they're compared to villains who are seen as genre-defying and revolutionary, it's hard to argue against the idea that these villains are the best parts of their games.
Valve arguably peaked as a game studio in the early 2000s, and Portal perfectly showed why. Not only did it push physics engines to the next level, but it introduced the world to GLaDOS: Aperture Science's coldly sarcastic artificial intelligence that went rogue, killed the lab's staff, and forced Chell (and players) to solve deadly puzzles.
Given Portal's lack of characters and reliance on puzzles, it was up to GLaDOS to carry the story and give the game its personality. Needless to say, she succeeded in every imaginable way. When it comes to well-written game villains who are both funny and scary, GLaDOS set such a high bar that even Portal 2 struggled to overcome.