I think part of Black Crusade's issue is that it didn't really didn't show how it was distinct. As is the setting is far too "Rogue Trader or Dark Heresy, but as the bad guys!" The setting sets the players primarily against other Chaos things (ok, and the necrons) and feels quite arbitrary and forced, a bunch of coincidences to make the game they want possible, rather than trying to think of a compelling independent setting. Feel this about all the FFG produced settings after Rogue Trader actually (though DW's kitchen sink setting has to be the most blatant).
I personally thought a much more interesting game (and more distinct) would have been to play as a conspiracy on an Imperial planet. You are conspiring against the Imperium from within. I guess one of the issues is that this would only really have justified a supplement for DH, rather than its own game line.