This question is for N'Zoth realm only.
I made exactly same poll on PvP subforum but the answers there were biased due to anti-cross-faction naturity of PvP realm.
But I think the problem is the NPCs, and the work required to make the BG work for mixed faction party.
For example, when running a mixed faction Shadowfang Keep, only one faction can open the door after first boss, because the rescued prisoner is hostile to the other faction, and does aggro against them, failing the scripted event.