So the big problem with this theory is that there was a BODY left over after the fight for people to see. People would have confirmed that it was Madara. Zetsu hadn't been created yet, so there's nobody who could do such a perfect transformation (and most Zetsu clones which use the transformation jutsu turn back to their normal appearance when they die, except the one who transformed into Kisame).
1) We know Madara met with Mu at some point. If Madara learned the body split technique, he could have split himself (not a clone, and would leave a physical body). This would also explain why older Madara was so frail and weak (because he had divided his strength in half)
Not impossible, although the genjutsu theory still holds. However, little is known about Mu, but judging from what we do know, he seems like a loner, yet highly caring about his village. I doubt he would have anything to do with Madara, unless Madara actually saw Mu use his body split technique and copied it. However, what type of tech is it? Does it use any element, etc? Too little is known about it, and given nobody else ever used it, it's likely to be his alone (just guesses).
2) We know Madara would have known Izanagi. Later, old Madara had only one sharingan eye after giving his rinnegan to Nagato. If Madara stole two eyes at some point and used one for Izanagi, he could have kept his "real" eyes and had one left over later to use after giving his Rinnegan to Nagato. Of course, we saw in the Danzo fight that the altered reality of Izanagi eventually fades away when the technique is used. But then again, Madara might have been better at the technique than Danzo was because Madara was a real Uchiha (but didn't have any Hashirama DNA to super-power it).
This is interesting, cause most people immediately deny izanagi as a possibility, but that is not the case. In their last fight, not once did Kishi show us both of Madara's eyes (with EMS). So it's not impossible, he had prepared another sharingan than EMS. It would also explain, why he only had 1, after giving his eyes to Nagato. It's impossible that he lost an EMS on Izanagi, since Nagato had 2.
However, the problem about this, is that as I understand Izanagi, it does not last very long before the person re-appears. So all your initial arguments bash this one, unless you use my arguments it could work. Although compared to Danzo it lasts very shortly, whereas Obito could keep it going for 5 minutes (or more).
Last I do not understand, how he could then use Susanoo, which is my main reason for bashing this theory.
3) He could have died and been revived later. Without the Rinnegan (which he hadn't unlocked yet and nobody else had) he could have used Edo Tensei or had one of his helpers use a sacrifice technique like Chiyo used on Gaara.
These are the only things I can think of that make sense.
Chiyo invented that technique as I remember, however, it's unlikely for Kishi to pull something new up from his hat. In fact it would just make it disappointing for the story, if he couldn't think of anything better. And usually he can