I have three footjoints for my Haynes - B, C and D. Without a doubt, the response on the low end of the flute gets worse the longer the footjoint is. In other words, low notes like D, E and F sound more open and resonant to my ears with the D foot, less so with the C foot and less again with the B foot.
That is not to say that I don't use the B foot because I don't like the tubby response of the low end, I do use it and use it fairly often. That's because low B is a very useful note, especially in jazz (and some 20th century stuff) - even if I think the flute sounds and feels "wrong" the entire time I'm playing it...
And lively as the D foot is, unless I'm playing Mozart, the loss of having a low C and C# can be frustrating too. So the moral of the story is that I look at the musical situation first, then decide which footjoint is best for the job.