I think it all comes down to what the fans want to see. A lot of fans have a hard time believing that Orochimaru is no longer a villain and is just more of a side character causing a few problems at the most. So, that being said, a lot of fans want him to be the main villain again since they feel like he was kind of shamed in part 1. The Shisui people just want it to be him because we have had little screen time with this character before his death and have heard great things. Like he's the greatest genjutsu user the Uchiha had at the time to the point where his eyes were hunted through out his adult life until they were taken/given away before his death. So, with that being said as well.. people think that his character didn't get much justice at all.
How I see it? Orochimaru had his moments in part 1 and early part 2 as the main villain (or side villain). His fight with the 3rd and then Tsunade showcased his many abilities and wowed us back then. By the time of part 2, a lot of the characters had gotten way stronger and he was also handicapped. He was kind of useless, so he was "killed" off. Now we look at part 3 (lets forget about the end of part 2 for the sake of time). Both Sasuke and Naruto are adults and far far FAR more stronger than they were in both part 1 and 2. Do you really think either of them would have a problem with Orochimaru at this point? Going off of what Naruto said, it sounds like Orochimaru is just a bother to him, not a pressing looming problem. He is more concerned with the new Akatsuki than he is about Orochimaru. So I honestly can't see the hooded man/woman being Orochimaru himself unless if Kishi wants to go 100% with his fanservice.
Shisui is out of the question because he was one of the only Uchiha that didn't fall completely to the curse. He wanted peace for his clan and for his village. He was also highly logical. If Shisui was who he was made out to be this whole time, he would understand where Sasuke was coming from and why he killed Itachi back then. He would have also been watching Sasuke this whole time and know that he isn't the same as he was when he killed him. That being said Shisui has no motive to kill Sasuke and call him a disgrace to the clan unless something happened between part 2 and part 3.
This all being said, I don't understand why some people don't believe that maybe in all of the chaos.. some Uchiha survived because they happened to be away (vacation, missions, etc). The cloak guy is speaking as if he is an Uchiha himself and this mystery child looks too freaky to be a real Uchiha.. but I guess only time will reveal the answers to us all.