First: In chapter 661-662 (I believe), the one where Madara stabbed Sasuke through the heart. He said earlier on that he'd gladly take his eyes for his own use until he regains his rinnegan. Well, he got one of his rinnegan eyes, but he still had 1 hole left. Why he didn't take one of Sasuke's eyes and used it untill he regains his other rinnegan? Also, we were always presented with how cruel Madara was and he himself states it during these chapters that whether it be his brother or son or etc he'd have to sacrifice them to protect something else (his dream in this case). Well, he stayed long enough to watch Sasuke dying, why he didnt decapacitate him in order to be sure he wouldn't magically resurrect and take his eye while doing so?
Second: The last time we see Madara is around Naruto vs Sasuke battle shortly before the sage disappears and what we saw was his corpse. If I remember correctly, Madara's body was very valued by the ninja world, black zetsu himself states that and as well Tobirama when he first 'died' against Hashirama. His body was taken into the woods and examinated, though he used that shadow clone to replace it with himself. Anyway... considering how Tsunade was experimenting with the white zetsu stuff and made Naruto new arm, Madara's body would be a world full mystery. His rinnegan, although deactivated, was still there, so what the heck happened with Madara's body? His fusion with the hashirama cells was also there, so his body could be exploited..?
Also on a side note I got a little fun theory here - Wouldn't it be fun (although it won't happen
) if the 'vessel' for the Kara turns out to be Madara's body (not himself as a person) and they use it for whatever reason they need it? 
It would tie up nicely with the original series, reminiscing but still keeping the new villains and all that. If I were the author I'd honestly pull off something like that.
Second: The last time we see Madara is around Naruto vs Sasuke battle shortly before the sage disappears and what we saw was his corpse. If I remember correctly, Madara's body was very valued by the ninja world, black zetsu himself states that and as well Tobirama when he first 'died' against Hashirama. His body was taken into the woods and examinated, though he used that shadow clone to replace it with himself. Anyway... considering how Tsunade was experimenting with the white zetsu stuff and made Naruto new arm, Madara's body would be a world full mystery. His rinnegan, although deactivated, was still there, so what the heck happened with Madara's body? His fusion with the hashirama cells was also there, so his body could be exploited..?
Also on a side note I got a little fun theory here - Wouldn't it be fun (although it won't happen
It would tie up nicely with the original series, reminiscing but still keeping the new villains and all that. If I were the author I'd honestly pull off something like that.