I use to think it was Obito, until I read the chapter when the Nine-tails attacked Konha the other day, it became evident that Obito couldn’t have been the masked assailant. In that chapter, you see Kakashi, Might Guy, Asuma and Kurenai as rambunctious teenagers who were eager to help defend Konoha, from this evidence, Obito could not have been the masked man, because Obito would’ve been shorter and younger than the masked man. I feel a little stupid now, because like the majority of people, still think Obito is Tobi, now knowing how strongly he isn’t, I find the folly of anyone who would still think it is Obito, although “nothing is true, everything is permitted.”
There are many theories on who it could be, I’ve heard of the Zetsu theory which is indeed plausible, but you’re asking for my own theory, but up until now, all my theories have been abolished. But I’ll throw in a far-fetched theory I just concocted. First I would like to begin by defining what Space-Time Ninjutsu is via Narutopedia:
Space–Time Ninjutsu (時空間忍術, Jikūkan Ninjutsu; Literally meaning “Time–Space Ninja Techniques”) are techniques that allow the users to manipulate the space–time continuum. By manipulating a specific point of space, the user can warp anything targeted into a dimensional void and teleport it to another location instantaneously.
I don’t know about you, but from all the techniques and jutsu that are categorised in Space-Time Ninjutsu, I see the element of space being manipulated, although I have not seen any element of time manipulation, which leads me to my theory. I think that the masked man is still in fact Madara Uchiha, although he may be indeed be from another time, or alternative universe. I don’t know much about Space-Time Ninjutsu, but I know it is about manipulating the space-time continuum, and this leaves many possibility that alternative universes may exist, because other dimensions do exist, since Tobi is very talented in Space-Time Ninjustu, where he was able to transport Sasuke and Karin into another dimension so Karin could heal Sasuke, during the Five Kage Summit arc. So that’s my best theory I could come up with, I can still be very wrong, but at least I try to be enlightened enough to make up my own reasoning.