Krang is the one thing about the old series I love more than the new series, the movies, and the original comics combined. Other than that, I really think the old version of Baxter Stockman was weak, and some of the toy monster mutant types were just added in to sell figures. Really. The new series Baxter Stockman was the best villain in that show. Especially Insane in the Membrane, which has become my favorite episode of anything now.There are some bad guys who I like better than the stars, like Boris and Natasha, Dr. Evil, many of the 1980s Teenage Mutant Ninja Turtles villians (particularly Krang), some of Darkwing Duck's enemies (Megavolt, Quackerjack, Steelbeak), King Koopa, Dick Dastardly and Muttley, Wile E. Coyote, and some others. And I often want them to win.
And there are other villians I like but usually don't root for. For example, I like Elmer Fudd better than Bugs Bunny, but I usually don't want him to defeat Bugs Bunny (there are the occasions when I feel sorry for him, most of which are in non-Bugs cartoons like Doggone People).
As for Elmer, I never viewed him so much as a villain as an antagonist. He isn't inherently evil (unlike Yosmite Sam), but he is a hunter, and a force against Bugs Bunny. Though, much as I love the wascally wabbit, he seems to deserve it now and then.
Now, it's hard to say a villain I don't route for, or at least prefer to the heroes or even like just as much as the others. Villains are usually the most interesting characters in the show. You think I watch PPG for the girls?
Now, off the top of my head, any villain in a Muppet Movie ('cept Piggy in Oz). Going up against any Muppet is true evil in my book. I'm not a huge fan of Glee, but that evil sports coach needs to be punished at the end of every episode ( where's Dokurobe when you need him?)... I really hated the pipe organ in the Beauty and the Best Christmas cheapquel, even though he was voiced by Tim Curry... come to think of it, I really disliked that whole movie. Dr. Wily in the video game only, especially when they do that hackneyed spaceship disappearing reappearing schtick... come to think of it, does ANYONE root for the bad guy when they're playing opposite him in a video game? But as far as Captain N and the Mega Man cartoon series are concerned, he's one of the best characters. Why, Scott McNeil's Dr. Wily is the ONLY reason to watch the Mega Man cartoon.
Oh, and anyone who was trying to kill King Kong in that movie. Sorry, but I consider King Kong to be the hero of the picture.