I think Giteau's non-selection is a positive move for Australia. I've mentioned a lot over the past few years that players like Rokocoko, Giteau, Spies, Smit, etc. have produced a series of performances well below what should be expected of them.
With regards the halfback, I think most teams will pick three halfbacks more as security than anything. Like the Cricket World Cup, replacements have to be permanent so if Genia has a slight injury, you can't temporarily fly Phipps and use him as cover, unless you replace Genia outright. Same reasoning behind three hookers for essentially one starting spot.
Elsom's captaincy is terrible so elevating Horwill is certainly a good move - should've happened about a month ago pre-Tri Nations though.