true enough. For instance, why didn't Tobi just come back a couple weeks later and take naruto now that he was the jinchuriki, or before naruto graduated the academy. This would have made his plans so much easier.just take the jinchurikis before they become ninjas, then stock pile them until you're ready to use them. but no, he waits until they're trained ninjas, and does stuff the hard way. Amateur lol
I wonder if Konan even knows where nagato is buried. I know we saw her taking nagao and yahiko's bodies with her.... yet then we see three mounds on the shrine for Jiraya (basically his grave). Which makes me wonder if Nagato and Yahiko were buried with their sensei???
he might not have come back because he might have had to lick his wounds, and he should have known that the jinchuriki who can not protect themselves would be protected by the village they live in, you have to remember that each village that has a biju will try to protect it, even if they fear the beast/jinchuriki. they don't want to lose it's potential power.
I'm guessing madara spent his time analyzing the jinchuriki and theyr fighting style as they developed and let them grow to a point where the villages might belive that they can hold theyr own. in the same time he formed akatsuki with some formidable members capable of taking on these jinchuriki.
that way he could chose the fighters so they have a good advantage over the jinchuriki and stay in the shadows himself.
and on topic, I doubt the would have burned the body, she said that the rinnegan is a treasure of the rain village, she would not burn them unless they were in danger of being lost and used against them. plus, nagato is one of her dear friends, I suspect she could not do it unless she knew it was nagato's own wish.