When I see things like this the first thought that comes to my mind is that the contenders are by and large too recent, we're looking at a competition that is largely pitting the animated movies of Generation X against each other, with nods to Generation Y's "Pixar" movies like Toy Story. The problem with this of course is that it overlooks things like "Snow White" and "Cinderella" which arguably started it all, set high bars for animation for pretty much forever, and most importantly have been watched and embraced by pretty much every generation since their release, in some cases setting sales records when they have been held back from public release and then re-released on video or in theaters. I'd say that while it's POSSIBLE that someone hasn't seen these movies, I'd imagine far more people have seen them and liked them than any of the modern contenders, especially if you start thinking globally.
When it comes down to things like the best Disney villain, consider that when all all the bad folks gather around at night (Disney crossovers are frequent) it's not Jim Walker or Jafar they look to for leadership, it's inevitably Malificent , the evil queen, a character that is both instantly recognized and absolutly oozes dark charisma, not to mention having been the bearer of one of the most dramatic beat downs to Disney heroes (and part of what is their best over all fight scene/confrontation).
Now, don't misunderstand this, I'm not actually breaking this down to a personal favorite, but saying there are some objective criteria that can be used. If your going to argue "best" at this time you need to look at classic disney, give it a few more generations and if Aladdin, Beauty and The Beast, or some of the works of Pixar are still around and being viewed the same way, then they would be due for consideration.
In closing, other than a certain evil Queen from one movie, how many of the Seven Dwarves would you recognize? The answer might surprise you, and I think you'll get more recognition from that, than Timon and Pumbaa no matter how praised "The Lion King" might be, at least for the moment. None of these works have endured long enough to be a true, multi-generational global phenomena.
So to throw my hat into the ring, instead of analyzing the match up, and talking about how it's subjective, you might want to kind of consider than the real match up probably should have been "Cinderella" against "Snow White".