I like the ideas presented in the VN with the people having different colored blood based on the territory they were born in. I enjoy the cute banter between the characters as well.

However, the writing needs to have some significant polish. The cutaways from serious situations is jarring at best and a mood killer at worst, especially the scene with Reuben and the sudden cutaway to explain the biology of this world's organism. The parenthesis could also be replaced with some meta writing style. For example: "He stands, unwavering, before asking a simple question (which will end in a full stop and not a question mark because that's how tired and monotone he sounds). " The parenthesis really break immersion and painfully shows that the writer is inserting themselves into the narrative. 

Now, an improvement could be: "He stands, unwavering, before asking a simple question, though he was so tired and indifferent that if it was written it would be without a question mark." And then the next statement would be much funnier since he's literally doing it and the MC is the one commenting on how monotonous Reuben sounds. Basically, have Neo stay in the driver's seat and trust the reader to figure things out via context clues. If you really need to define terms, please provide a separate dictionary that the reader can refer to in the game.