Alter AILA/WMG

The reason Celia thinks that Indy is lying about her age isn't because that she thinks she looks too young, but because she looks too old.
Sounds crazy, but think about this. Celia, like in the original, is heavily attuned to psychokinesis, including being able to see peoples' "auras". She would probably consider the mind more important than the body, so would go by someone's aura to indicate their age. (She herself claims to be six despite looking 14 or 15) The fact that she immediately asks Jake if Indy uses skincare products to make herself look younger adds suspicion to this theory as well.

At the very least, there must be something important about that cutscene, as the dramatic BGM indicates. Perhaps we'll need to wait until Variant... :( (I have suspicions that resolution to that subplot was supposed to be included, but was cut due to Development Hell problems, like with Hawk and Dread's backstories)

Alternatively, if she does think Indy's too young, she's thinking in terms of whatever her own species' aging rate is, and since she's six by her standards but 14 by ours, someone claiming to be 13 would be someone in their mid-20s or 30s by our standards.

Indy is a variant.
A corrally to the above theory. Indy's elemental weaknesses and resistances are very similar to Aila's -- 25% resistance to four elements, 50% weakness to another. She is the only character to have such a resistance layout, and the similarity is rather suspicious. Furthermore, she possesses incredibly unique and powerful psychokinetic powers. (She is probably some form of a weaker variant, though, since Aila is still far stronger than her -- maybe a human infused with massive amounts of psychokinetic energy?) She is definitely a very strange character. If the above theory is correct, perhaps Celia thought she looked too old because of the huge amounts of energy radiating from her?

Indy is the little girl mentioned in the Orbital Prison's Apocalyptic Log.
Word of God has directly Jossed my original guess (Aila), so my next best guess is Indy. Think about it -- Erin never really talks about where she came from, just that she's an orphan. It's possible that she was found alone somewhere in Pallas after the Prison crashed, and picked up by people who assumed she was an orphan (although why she was dumped into Stynx raises further questions). Could work with the above theory; perhaps they were experimenting on infusing the powers of a variant into a human, or trying to mind-wipe and imprison a dangerous variant? (Maybe the others in the core were other variants -- Nightmare too, possibly?) At the very least, Word of God has promised an explanation of what the Orbital Prison is (and the Backstory surrounding it) in Variant, so we'll know one way or another.

The characters that will be dropped from the roster in Variant are...
Neok says that not only is he reducing the amount of playable characters to six in Variant, at least three of them will be new. That means at least four characters from the original will be dropped. My bet's on Jake, Gray, Violet, and either Erin or Leon. (If five characters are being dropped, both of them) Indy is obviously staying because she's the protagonist, and Celia sounds like she'd still be very important plot-wise. (They'll need her if they encounter more variants, after all!) Erin obviously has an important connection to Indy, and Leon was the previous protagonist. Jake is probably the most likely to be dropped -- I can see him opting to go into Mission Control instead of field work, as would Gray. Violet is the least central to the plot -- most of her ties were to Ceres, so I can't imagine her having a lot of plot influence.
 * This has been resolved now that Neok has revealed the returning characters -- they will be and.

One of the new playable characters in the sequel will be a young variant.
They can't all be Exclusively Evil, can they? I think it would be very interesting to have a variant be a playable character, possibly a young one, and could be used to start a lot of plot threads or character interactions. It might also create tension with Aila (who will doubtlessly resurface and possess Indy), since it wouldn't want to kill one of its own kind, but would also realize Aila's crazy and has to be defeated somehow. It's also possible that Aila might convince it to join her side, leading to either a Heel Face Turn or Heel Face Revolving Door, depending on which side it was on to begin with.

So many possibilities! Which is why I think it might be included.

The reason variants are emotionless is due to their composition.
Humans are physical beings, but variants are just conglomerations of mental energy. This means that they're essentially a disembodied mind, and the mind is often said to be the source of reason and thought in ancient philosophy. However, because they aren't physical beings, they also lack souls/adrenaline/whatever, which is necessary to form emotion. The end result is that they're very good at reason and logic, but cannot express emotion.

Every single route of Alter A.I.L.A. and Alter A.I.L.A. Genesis happened as a variation of Groundhog Day Loop.
Rebel, Imperials and Independents routes happened in first iterations of loop, and as we all know, none of them ended well. Those who played Innovator route noticed that, what was a moment when route started. This all was caused by some Being that wanted to help Blue reach ending of Innovator route. This theory also goes with Grey’s theory.

So we can assume that Being’s goal was to allow Blue to save the world of Alter A.I.L.A. and accomplish his original mission. The outcomes of first three routes couldn’t allow to this, so Being helped a little and triggered Blue’s decision that lead him to the Innovator route. Because of route's Bad Ending this also didn’t work, so on next iteration of loop Being once again helped, what finally lead to desired outcome and Blue was finally ready to accomplish his original mission.

But this still didn’t work and after events of Alter A.I.L.A. Blue has failed. That’s why Being realized that to lead Blue to desired destination bigger changes were required. And that’s how was created the world of Alter A.I.L.A. Genesis. This worked so well that it leaded to desired outcome in the very first iteration of loop.

And who was this mysterious Being? This same person that Blue/Leon could encounter only once in all loops of Alter A.I.L.A., and once in Alter A.I.L.A. Genesis,.

Leon and Gray are part of a highly psychokinetic human-like race at war with vast amounts of Variants.
They both came from space and have several odd traits. For example, Leon's Ether Round and Killing Point, where his eyes change colours, suggest some latent powers, not to mention the ease with which Aila controlled him hints at him having some sort of psychokinetic aura. As for Gray, his second Exceed ability, Dark Force, is proof enough that there's something about him that's VERY different from others. As for the war part, this is mainly due to the fact that Celia is of such importance to them. After all, she can negate the field created by Aila, and, being actually six years old, must have been bio-engineered as some form of last hope to fight off other variants with such powers, which is most probably why her existence was supposed to be such a great secret, being of critical importance to complete Leon's original mission and end the war.
 * Your phrasing is odd; isn't the fact that they're at war with something explicitly canon? Gray states it outright (as well as Celia being a bio-engineered weapon that is crucial in said war). From Gray's description of them though, Variants sound rather rare, and even one of them takes incredible effort to take down, so I don't think there would be enough of them to form a full-scale war. (Also, what do you mean by Leon having a psychokinetic aura? Everyone does, according to Celia.)

Aila is dormant inside Indy and will try to manifest herself in Alter A.I.L.A. Variant
After being what amounts to be eaten by Indy, and seeing that blue flash in Indy's eyes, we can only presume that Aila is still somewhere in there, though vastly weakened. So, for the next 3 years between Genesis and Variant, she will feed off Indy's inherent psychokinetic powers, trying to restore her power, perhaps eventually taking control of Indy, though not without showing some signs as to her presence (IE:dreams, nightmares, "sleepwalking", temporary possession...)
 * Taking into account the Golden Ending of the original Alter A.I.L.A., I'd say that this is practically canon. I also believe that it is extremely probable that Aila will return as a major villain in Variant (probably during a late-game arc where you have to kill her for good by "exorcising" her out of Indy, similarly to the Leon battle in Genesis).

Leon and Gray's species can manifest Superpowered Evil Sides to use very powerful psychokinesis, in this case Killing Point and Dark Force.
Just look at the animations for them. Dark Force is freaky enough, but Killing Point also makes Leon's eyes fox-like, and glow, in addition to the fact it's Cast From Hit Points. Something bizarre is going on here. (At the very least, this will be answered for certain in Variant -- Neok promised he'd explain them.)

Arbitrary Gun Power is justified.
It's entirely possible that people can use their Psychic Powers as shields to defend against normally lethal weapons. Getting hit wears the shield down, which is why characters with zero HP are "wounded" instead of "dead" -- their shield was broken and their physical bodies were actually hit. This would also explain why healing items are called "stimulants", and how people can dodge bullets (using the same powers).

For other enemy types, mutants are immune to Force, so I would presume that even if they don't have Psychic Powers (and some do), they're just naturally tough enough to withstand such attacks. Robots are obviously much hardier than squishy humans, and it's never really explained what "???" creatures are, but they're probably in the same boat as humans or mutants.

(Yes, I am aware that this entire WMG is basically "A Wizard Did It"...)