CodeKyuubi said:
They're no different from vector images, aren't they? As Ars said, they should be parented to the original, and I think there is meaning in uploading good upscales of smaller images.
Third-party edits are generally not allowed. Exceptions exist though, such as scan fixes like detexting and removing creases, or colored versions of images, like the colored To Love-Ru manga pages, or pixiv artists coloring other artists' lineart, etc.
Vector traces are mostly crap, but if done properly, they can have some redeeming qualities other than larger image dimensions (e.g. transparent background and gradients) and that may warrant keeping them. An upscaled image on the other hand, is just that. Allowing them might open the floodgates to people upscaling and uploading whatever en masse, and that's just useless clutter when you have the original image and easy access to an automated tool, like S1eth said.
That being said, the tricky thing with waifu2x is that if an image has the usual anime flat colors and no realistic textures and details, the upscaled version can easily pass off as a genuine larger version, especially if the approver isn't familiar with the original and doesn't spend too much time examining minor details.