Skype with both system and microphone audio in El Capitan
I have just done this - for skype recording and it works:
My settings are almost identical to yours except: -

in skype I have the microphone as my mic - not as the aggregate device.

I have also added my headphones (!) as part of the multi output device. ie headphones + built in + soundflower (2 chan)

I can now record the entire skype video + audio + the mic input from my end using Quicktime screen recording with the mic input set to the aggregate device...

nb - no "flowerbed" used, no "line-in" used