C'tron isn't just a biologist by trade, he's genuinely intrigued by living things in general. Assuming that he and Sidwell are one and the same, it could go a long way in explaining the latter's motivation. Sidwell not only bankrolled Lea's creation but took a personal interest in her development. Even his mistreatment of the other Evotars was ostensibly for the purpose of funding future experimentation and research. For someone so interested in the miracle of life, what could be more exciting than creating an entirely new lifeform?
Speaking of C'tron being Sidwell, there's also the matter of the Lukas Evotar. Lukas is a nice person who is of help to the newer players, even though he is of higher level than them, and even as they catch up, he trusts them to pull their weight. C'tron had to observe Lukas in the early day of his joining the First Scholars so that he would have all the data he needed in order to create an Evotar to keep Lea stable during Project Trackwalker Red, and he may have given Lukas the idea to recruit Lea and Emilie into the guild as a means to monitor Lea until Gautham could secure her once again. There's also the matter of talking with Emilie about Lea's sudden disappearance afterwards. When you put it all together, Sidwell had his entire plan for Lea prepared from the start; he just didn't count on Sergey staging a revolt against him through Lea.
Shizuka's hatred towards Lea may seem excessive, but it may be fueled by personal issues. Of note is that she was initially the most enthusiastic member of the team to accept Sidwell's offer... which eventually led to her brother's death, the loss of her freedom, and the suffering of dozens of innocent beings. Furthermore, Sidwell's plot wouldn't have been viable without her contribution, as Lea simply wouldn't exist without her. The clincher is that when she finally buries the hatchet with Lea, she tearfully notes that "[you're] not like me at all". The verdict? Shizuka is suffering deeply from self loathing, and viewed Lea as an extension of herself that she could lash out at. When she screams "This is all because of you!" she's yelling at herself through Lea. Her reconciliation goes hand-in-hand with her realization that Lea as a person in her own right, and more than just a shadow of herself.
If this is true then it adds an extra layer of symbolism to Shizuka and Lea's duel. It ultimately dosn't matter who wins or loses; neither one can destroy or deter the other, so they just keep fighting endlessly until they are interrupted. Taking this as a metaphor for self loathing, no amount of inner abuse will change your perception or bring you peace (the music that plays during this segment is even titled Endless Frustration). The only "victory" is to stop fighting long enough to make peace with yourself.
In the Vermilion Wastes, you can find an NPC running headlong into a wall while mumbling about "getting out". For most, this would seem like a typical bug, but for savvy gamers it is a clever bit of foreshadowing that the "NPCs" here are more than what they seem. The act of sprinting into a wall to access forbidden areas is a popular form of "glitching" (one that Lea herself exploits in a later quest), something a mere program would never try.
The choice of the Spheromancer class for Lea's—and by extension the player's—class. Spheromancers are described as being the 'Jack-of-All-Trades of Cross Worlds, whereas the other 4 classes all have their specialties: Pentafists with melee, Tribladers with dash, Hexacast with ranged and Quadraguard with... well, guarding. By using a Spheromancer, the player is able to experience all four aspects equally.
The Henry quest chain eventually ends with the reveal that it was a questline designed by a white-hat hacking organization that assisted the game's developers in discovering exploits during the game's early days. Which seems awfully strange, since all the NPCs involved act like actual humans, especially compared to other NPC characters. In fact, the "moderator" NPC even recognizes Lea's speech module problem and adjusts his instructions to her accordingly. However, this makes a lot more sense if the questline was entirely designed and written by the aforementioned organization, who wanted to create a believable scenario where even players could be fooled into thinking that Henry and the moderator are real people, giving them significantly more depth in terms of ability to respond to players and even taking into account the fact that there are players with speech module issues. It's very much an in-universe example of Developer's Foresight.
Horror
As pointed out by Joern near the end of the game, Lea remains remarkably idealistic and upbeat in spite of all the painful experiences she encounters during her journey. Since Lea was "born" using Shizuka's mind as a template, she probably inherited her emotional resilience from her. Yet less than a year after Lea's creation, Shizuka has become bitter, cynical and abrasive to her friends and potentially hostile toward everyone else. One can only imagine what she must have seen and experienced under Sidwell's thumb, or how deeply her brother's death must have hurt her for Shizuka to change from someone resembling Lea to the Broken Bird we see in the game.
The canon Good Ending raises some implications that border on Existential Horror. In spite of the Evotars being allowed to exist, they are stuck in the game and can never return to the lives they remember that were never really theirs to begin with. It is possible that they will be stuck like this forever. Also, being sentient computer programs, they probably do not age and are functionally immortal as long as their data is preserved. Even if a means of allowing Evotars to live outside of the game is found, that still doesn't change the fact that Lea's friends are human and will die at some point. So her friends will die, and she has to contend with (depending on how you read Lea and Emilie's relationship) her closest friend or the love of her life growing old and dying, while she won't age a day. And if a means of exporting Lea from the game isn't found, she will be stuck in the game even after its userbase starts to decline, leaving her stuck in the world of a dying MMO that the people in her life will eventually move on from. And all of this applies to all the other Evotars as well.
