Well, one possibility which occurred to me during work yesterday:
When do they start playing Sburb? Specifically, how old are they at the time, and at what point is it in the NGE timeline?
In Homestuck canon, the game begins on the youngest player's thirteenth birthday, and they've all been in (electronic) communication with one another for years. (And there are four of them, giving rise to the second manifestation of the recurring but possibly meaningless number 413 - the first being April 13th, the date on which the whole thing began.)
If you set the Sburb session as beginning sometime before NGE canon, possibly years before, that would turn things on their heads... and it would give you the chance to include anything from just the three primary pilots to all of the potential Children, meaning IIRC the entirety of their high-school class (and Kaworu), with less elaborate justification.
Note in passing that you'd have to come up with some reason for Rei to be playing the game; you'd have to take that into account no matter when you set it, but if you set the events prior to the start of canon, the only obvious reason for her to do it is if Gendou either ordered it himself or accepted someone else's suggestion that it happen - and there's no obvious reason for him to do either one of those things. (The same applies to Kaworu, from different sources.)
Note also that no, you don't necessarily need even male/female ratios for post-apocalypse repopulation.
For one thing, since a Sburb session leads to not only the destruction of the world but also the creation of an entire new universe, complete with its own inhabitants, the question of repopulation may be moot in the first place.
For another, consider where the Sburb players (and their parents/guardians - one total for each player) all come from to begin with, at least in both known examples from Homestuck canon: they were created during the game by genetic recombination of the players/guardians into "paradox clones", which were then sent back in time to become the originals. Leaving temporarily aside the question of what that means for the Children's parents/guardians, there's no theoretical reason a less self-referential version of the same thing (much as is used in Homestuck to breed the frogs) couldn't be used to add more people in after the whole thing's over, either to even out the male/female ratio or just to effect repopulation directly.
However, even with the parts I haven't brought up yet, that's still only half of the equation. How does NGE canon, and specifically NGE cosmology, fit into all of this? The Angels and the Progenitors, at the very least, have to be taken into account somehow, and the concept of the AT field possibly does as well... even if the entire thing is ultimately subordinate to the Homestuck cosmology, we still have to know how it all works and where everything fits.
I don't have any real suggestions on that front. I can imagine something tying the Angels to the Denizens, and/or the Progenitors to First Guardians (except that there's only supposed to be one of those per session-world, and the ones we know about are powered by the Green Sun, which is intimately tied to the events of Homestuck canon and to the two canon sessions), but it's hard to make the numbers work out and I don't have any details.
When do they start playing Sburb? Specifically, how old are they at the time, and at what point is it in the NGE timeline?
In Homestuck canon, the game begins on the youngest player's thirteenth birthday, and they've all been in (electronic) communication with one another for years. (And there are four of them, giving rise to the second manifestation of the recurring but possibly meaningless number 413 - the first being April 13th, the date on which the whole thing began.)
If you set the Sburb session as beginning sometime before NGE canon, possibly years before, that would turn things on their heads... and it would give you the chance to include anything from just the three primary pilots to all of the potential Children, meaning IIRC the entirety of their high-school class (and Kaworu), with less elaborate justification.
Note in passing that you'd have to come up with some reason for Rei to be playing the game; you'd have to take that into account no matter when you set it, but if you set the events prior to the start of canon, the only obvious reason for her to do it is if Gendou either ordered it himself or accepted someone else's suggestion that it happen - and there's no obvious reason for him to do either one of those things. (The same applies to Kaworu, from different sources.)
Note also that no, you don't necessarily need even male/female ratios for post-apocalypse repopulation.
For one thing, since a Sburb session leads to not only the destruction of the world but also the creation of an entire new universe, complete with its own inhabitants, the question of repopulation may be moot in the first place.
For another, consider where the Sburb players (and their parents/guardians - one total for each player) all come from to begin with, at least in both known examples from Homestuck canon: they were created during the game by genetic recombination of the players/guardians into "paradox clones", which were then sent back in time to become the originals. Leaving temporarily aside the question of what that means for the Children's parents/guardians, there's no theoretical reason a less self-referential version of the same thing (much as is used in Homestuck to breed the frogs) couldn't be used to add more people in after the whole thing's over, either to even out the male/female ratio or just to effect repopulation directly.
However, even with the parts I haven't brought up yet, that's still only half of the equation. How does NGE canon, and specifically NGE cosmology, fit into all of this? The Angels and the Progenitors, at the very least, have to be taken into account somehow, and the concept of the AT field possibly does as well... even if the entire thing is ultimately subordinate to the Homestuck cosmology, we still have to know how it all works and where everything fits.
I don't have any real suggestions on that front. I can imagine something tying the Angels to the Denizens, and/or the Progenitors to First Guardians (except that there's only supposed to be one of those per session-world, and the ones we know about are powered by the Green Sun, which is intimately tied to the events of Homestuck canon and to the two canon sessions), but it's hard to make the numbers work out and I don't have any details.