Here's a repost of my thoughts from a page or 2 back:
I figure it'll end up somehow being Izuna too.
I used to think it might be Sasuke's father because whoever Tobi is found out that Kushina was pregnant and how far along she was, which allowed him to plan everything perfectly. During that flashback, Kushina talks to Sasuke's mother, and she's aware of Kushina being pregnant even though that information was supposed to be on lockdown. So if Tobi were Sasuke's father, he could've easily found out that information through his wife. Also, he could've easily faked his death at Itachi's hands by having a Zetsu clone die in his place, and no one would've been able to tell since Zetsu clones don't disappear like shadow clones. Still, Tobi showed Sasuke his face after Sasuke's fight with Itachi, and I doubt Sasuke would have failed to recognize his own father, unless he was under a genjutsu.
Or Tobi could just be a Zetsu clone that Madara used his sharingan on to make the clone believe that he actually is the real Madara Uchiha. It seems like Madara has always been jealous of Hashirama and his "Will of Fire," so making a clone of himself would have allowed his own will to be carried on after he, the real deal, died. We've seen Tobi's body parts have some type of goo dripping from them after he has gotten injured, so that lends some credence to the Zetsu clone idea.
But yeah, in the end, I imagine it'll end up being Izuna. Izuna was supposed to have died in battle sometime after giving Madara his eyes, but his death could've just been a genjutsu cast by Madara on any witnesses. Then, after Madara died, Izuna could have retrieved his eyes and transplanted them back into himself. This would've allowed him to have the eternal mangekyo since it activated after Madara originally took his eyes, while losing the rinnegan that Madara achieved since Izuna didn't have Hashirama's cells implanted in his own body.
You know, it will probably be none of this and end up being some kind of wacked-out nonsense.