I have finished the game as yes-man with the brotherhood of steel, i went back to before the last quest to end it with NCR, i got to a quest that required me to "deal with" the brotherhood of steel, speech being my highest valued skill,i was hoping to diplomatically solve the situation, i found out i could not diplomatically ally the two faction with the new elder in place. this does not make any sense considering the new elder is supposed to be more open minded (thats the reason i did the quest to put him in) i should be able to get the truce between ncr and BoS with the new elder this should be fixed in a patch.
It actually makes a good bit of sense. Hardin wanted to open up the bunker without knowing whether or not the NCR was still hunting the Brotherhood and trusted an outsider to help him oust McNamara. The first thing he does as Elder is send you to kill the Van Graffs. Not because they're crooks and psychos, but because they're selling advanced weaponry. This clearly isn't a person that is interested in dealing with the outside world as equals.
It's subtle, but I felt the game made it clear that Hardin wasn't the diplomatic choice for Elder.