Sorry little bit late but having very busy time with work.
Directive/2004/38/EC says:
What exactly did you ask the MoJ? I am not sure if I understand this short extract, and I am very curious!
I asked is there any fee for eea family permit appeal?
and pointed out appeal legislation too
In reply got answer yes there is appeal fee as directive is not working directly in the UK.
personally I think as there is nothing written in directive either EC treaty that any member state charge for appeal fee, the only information given is about "processing time" and permit "issuing fee",
Might be that's reason member state can get benefit.
EUsmileWEallsmile says:
If you've been affected, had a successful appeal, don't take it on the chin, fight for your pennies.
I got no result yet but i will go further, and yes I agree need to fight for even single penny(ies), 39 million cost doesn't mean cover from appeal and misappropriate refusal due to misapplication of rules.