I've recently upgraded to After Effects CC from CS6 and I discovered that in the render queue, options for wmv and H.264 have been deprecated. I know codecs come and go, but I'd like to understand the reasons why Adobe eliminated these options. I know they're still available in Media Encoder CC, but why not After Effects CC?
While I'm not aware of any release of the official reasons for this, I can offer a strong theory based on my knowledge of the way workflows are intended with After Effects. After Effects is an effects and composition package, it is not designed to be placed at the end of a processing pipeline, but rather in the middle of it.
After Effects is designed to work on clips that will be edited in to a finished product. As such, it doesn't make a lot of sense to export from After Effects in a format that is targeted at end viewers, such as h.264 or WMV. It makes much more sense to target high quality, low compression intermediate formats that will minimize iterative quality loss or simply to use embedded compositions directly in Premiere.
Since it isn't a designed use case to be doing final output from After Effects, it doesn't make a lot of sense to put in extra development time maintaining a feature that is redundant and not part of the main intended work flow of the product. If you want to do a final output in that format, you can still use Media Encoder to do it and then they only have to license and maintain the encoders for one application rather than two.
It is unfortunate in the cases where you wanted to do a one off render of a clip, but that isn't their main use case that they are designing around. They probably decided that maintaining that use case simply wasn't worth the cost of maintaining.