See this for an explanation for the change regarding H.264, MPEG-2, and WMV and for the recommend workflow:
using Adobe Media Encoder to create H.264, MPEG-2, and WMV videos from After Effects
See this for an explanation for the change regarding FLV and F4V and for the recommended workflow:
removal of FLV and F4V export features from Adobe Media Encoder, After Effects, and Premiere Pro