Board Thread:Theories and Speculation/@comment-5413572-20151114042410/@comment-1210805-20151114073450

His whole body would have been valuable, but it's so far in the past of the Naruto world that it would likely have decomposed beyond usefulness by the time the series takes place. The only one who would have had any use for it would be Zetsu, and as far as I know he couldn't take control of a dead person the way he did to a weakened Obito.

What he needed was someone with Hagoromo's chakra, and the full Shinju, which Madara achieved. Presumably Zetsu wasn't able to manipulate Indra, or any of the earlier transmigrants to use whatever remains Hagoromo left behind. I also wouldn't be surprised if Hagoromo had the foresight to ensure that his body/eyes/remains could not be used when he died.