I think it's best for us all to download the files with the names like "Minitokyo.Anime.Wallpapers.Name_Of_The_Anime[number_of_file]" just like it was before instead of only the [number of the file]... its too much easy to organize and to know of what serie it is.
Why that change was made? Anyone could tell me?

Take a look at this existing thread: http://forum.minitokyo.net/showthread/18417/

Remember to search before you post in the future to avoid creating duplicate threads

I don't know but I usually change the name to suit my collection of wallpapers anyway so it isn't that bad for me.