Placing JFA is near impossible, because Cases 1-3 are legit bad. I mean, wow. Sure, Case 2 is relevant to the series as a whole, and its plot is resumed in the fantastic finale to T&T, but still, Case 2 of JFA just still ain't fun. However, in my opinion Case 4 is without a doubt the best case in the entire series. It stands head and shoulders over the rest. I absolutely love that case and the way that it deals with the characterization of Phoenix and the side characters, plus it told a fairly powerful message about what it means to chase the truth, even in a wacky court scenario like the AA series has.
Just a weird game in that regard, really.