Let me add information to the post
The media coder still outputs flv.
The real problem for me is that PPro no longer reads in flv – it is declared an unsupported format. This is where I am currently stuck, although I expect support for writing out flv will end soon too.
The reason I use flv is to create titles from AE for PPro and I use the alpha channel. FLV is the only output format from the media encoder that expressly presents the option to encode the alpha channel. So I do not care about FLV itself, just the right way to export titles.
So – how do you guys generate your titles in AE that you use in PPro? That is really what I want to do!