I think because he knew there was no alternative - I put it down to having to leave Pegasus and do it while being separated from his team and the others. As for S5, I always thought it was Joe's way of playing Sheppard's arc since Elizabeth was gone. He didn't want the command because he may have felt that was the best way those not so partial to him would have to get rid of him, so he declined but took on every bit of the moral responsibility for Atlantis. If it was Joe's intent to play that progression in that manner, to become increasingly menacing, protective, worn down... I'd say he aced it. Not like TPTB were giving him any direction.
That's what I think too. That scene where they send repli!Weir to the gate is heart-wrenching, because he's completely shutting down at that point. When she was dying the first time, he got teary-eyed, but it was like he was beyond tears in season five.
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