I’ve also noticed the graininess of the Animation codec exported out of Adobe Media Encoder – even at 100%. Used to frequently use this as my standard intermediate codec, but it’s unusable as exported by Premiere.
Maybe someone knows of some setting to fix this? There don’t appear to be any codec options available for Animation in the Adobe Media Encoder. Have resorted to Photo JPEG as a fallback. Of course, this doesn’t help if you need an alpha channel.