Sorry about the crappy title, didn't want it to be a spoiler title..
There are a couple of reasons why I think Aya would be back in a sequel.
1) If you read the note on Augustus Vassel, it states: "Louise Brier extracted from his body a particular gene belonging to an unknown twisted-one that gave him the power to come back to life." So....that's intriguing, it opens up doors to many possibilities, but again for Aya if she really doesn't have a body to come back to life, who knows..
2) I feel like there's so many contridictions in the story that there has to be two different timelines. My best example is in the dream Eve has in Episode 4 a scene shows Aya standing over Eve with a gun, and looking pretty serious (not all cry baby like Eve in the ending) and Eve seems to be not moving on the ground. I don't ever ever remember seeing this in the ending. I think this has to do with the updated file of Aya after beating the game once (under episode 6 CTI members). It states: "Eve's abilities suddenly awoke and ran amok. Aya tried to suppress them, but to no avail. She ended up shooting Eve Brea. The fragments of Eve's body brought forth the High Ones." So if Aya shot Eve, Eve would be dead right? And Hyde even told Aya at Episode 6 that she shot Eve (was it a lie? I don't know). It wouldn't make sense that Eve would have overdived into Aya because in the ending, the only reason she overdived into Aya was to try and save her. So Aya would have technically be the main character in the game and not Eve. Another thing I noticed in the ending that might allude to the many worlds interpetation is when Eve first dives into Aya and she has the gun in her hands, after all the SWAT guys are shot. But then, when Hyde is talking to Eve and stuff, a scene is shown where Aya is crawling to the gun, and she points it at Eve (who is still in her body), then she shoots the guy rushing her. Essentially, those are two different scenes because in the first scene where Eve dives into Aya, Aya never points the gun at Eve, nor does she crawl towards the gun. Maybe it was a continuity error? I don't know. Additionally, when you first meet Maeda, and select to talk to him about Eve, he says that she exist and doesn't exist all at the same time. Which kind of confirms the many worlds interpretation that there are parallel universes. So I believe that according to the Many-Worlds Interpretation, which is stated in Maeda's 1st email after beating the game once, there are two worlds, and the whole where Aya shot Eve was in one world, and the ending where Eve overdived into Aya (and supposedly killed her), and where Aya had Eve kill her was in another world. So pretty much Aya is alive in one world while Eve was not, and vice versa.
So for the secret ending, I think maybe those two worlds finally came together, thus having the possibility of Aya and Eve together in the same world, and somehow they knew the events that occured in both worlds...prompting Aya to say happy birthday to Eve (yeah, kind of farfetched I know).
But as for the secret ending where everyone suddenly dissappears after Aya says happy birthday to Eve, it could be depicting the weak coupling phenomenon that is possible in the many world interpretation in which there chance that the two parallel universe can communicate with each other. And there are a handful of studies that agree with that theory in that energy transfer is possible between the two parallel universes. So I think that's what happened in the secret ending...like the coupling effect was pretty weak that everyone suddenly disappears because they didn't belong to that universe.
I think the two worlds split right when Eve's body started to deterioate, after Aya got shot perhaps. (maybe another reason Time Zero is called Time zero?) And one world is when Aya shot Eve to stop it, and another is when Eve dove into Aya. And in the game, I guess we're in the universe where Eve exists.
And another contradiction is that in the dreams, you see it in Aya's view in that it shows Eve's face being very concerned about Aya. If it was Eve in Aya's body, how would that even be possible? Unless for some reason Eve takes up some of Aya's memories after overdiving into her.
Anyway, now that I think of it, if the story does revolve around the many worlds interpretation, it's still science based, although more physics and quantum mechanics than biological science like PE1 and 2. You know, if they make a sequel, and it turns out it was based on the many worlds interpretation....I'll be super surprised... but at least Aya would be back . But better not be having them explicty separated in two different worlds.
I think my theory is unique, I haven't seen it anywhere, and it seems to make the most sense (to me at least). So take it with a grain of salt.....
Edit: There is another possibility that the whole story was a dream, by Eve perhaps. There has been dialogue in the game that sort of hints at that. In Episode 2 when you go up to Blank, Hyde and stuff when you're back in the CTI headquarters, Blank said that Aya seeing the boss dead and Cray alive (before she changed the past that caused Cray to die) could have been all a dream and that it didn't really happen. And also Maeda's emails use the wizard of Oz theme in them. And we all know that in the story of The Wizard of Oz, it was all a dream. Also, if you completed the feats for Episode 2 and is able to get the shower scene at the beginning of Episode 3, after the shower, Aya says that when she dove into Gabrielle, she saw some of her past, and wonders if it was a dream. There are so many dream references, that I won't be surprised if Eve dreamed up the whole twisted thingamajig.
Also I think it's a dream because what doesn't make much sense is in the ending where Eve dives into Aya, but Aya makes Eve shoot her. What doesn't make sense is that if Eve already dived into Aya, wouldn't that have already made the twisted(of course, unless Hyde is lying that Aya's soul created the twisted)? And what good does it do if Aya is shot by Eve if Eve already overdived into Aya thus creating the twisted? So perhaps Eve dreamt that up so she can have a way to look like Aya?
She could dreamed that she wanted to be so much like Aya that she made herself Aya.... That would explain why in the secret ending, Aya is taller than Eve (if Eve did infact take over take Aya's body, there shouldn't be a height discrepancy).
I don't know. Everything was fine/able to follow until the ending.