In the beginning, The Simpsons had two store owners: Apu and Comic Book Guy. Apu would sell anything at the Kwik-E-Mart to make a buck, and Comic Book Guy was an overblown tyrant who'd sell any collectible to make a buck.
Thing was, as time went by, people started to feel guilty about Apu. As an immigrant from India, you could tell that they were a little uncomfortable mocking the American dream so much - here was the guy who came from another land to open up his own shop! Isn't that worthy of being more than just a bit gag?
So they started asking a vital question: "Is there anything else about this guy we should know?" And as it turned out, yes. They started writing episodes that opened up his character - he wasn't just a ripoff artist, but a psychotically hard worker! And a devout Hindu! And proud of America! And a vegan! And a Ph.D. in Computer Science! And now Apu has a wife and too many children, and his relationship has been the focus of more than a few episodes.
They kept deepening who Apu was until he had depth. He's always got his roots in that stereotype of the Indian store-owner, but they've kept adding to him until he's a character in his own right. Because, I suspect, it felt unfair just to leave him stranded as nothing but a stereotype.
Comic Book Guy got no such save.
Comic Book Guy's been the focus of a handful of episodes, but the same could be said of almost any Simpsons character - after 400+ episodes, they're desperate for new plots. But his central character hasn't changed: desperate for women, a blowhard, lives in a basement, has no social life. And, I'd argue, it's because the Simpsons writers (and people in general) feel that the guy at the heart of the Comic Book Guy stereotype largely deserves his fate.
And I can't deny that. I've known too many Comic Book Guys, with their shops and lousy business practices and their focus on making themselves the king of their local nerd cabals rather than running a good business, and I'm pretty much in agreement that they're all just worthy of being mocked relentlessly. Apu got a bad break, and should have been fleshed out. Comic Book Guy? Well, he chose that path. He deserves nothing but mockery.
I just find it interesting that one stereotype got explored until he was a fully-realized character on his own, and the other remains a walk-on gag to say, "Worst. X. Ever."
(Full disclosure: my daughters say that I sound like Comic Book Guy, so feel free to read this entire rant in Comic Book Guy's voice. It's funnier that way.)