Generally I don't have a problem with fadeouts. They're just fine for a lot of songs. When a proper ending is added for live performances of a Genesis song that fades out in the studio version, I tend not to consider it an improvement.
That said, "Congo" easily has the most objectionable fadeout in Genesis history. It leaves the song sounding incomplete. I think it still could have been faded, but at a different spot -- say, after a return to the chorus.