Okay, feedback time. Forgive me, I'm probably going to ramble. A lot.
First, I have to congratulate you for keeping this story alive for 3 long years. That is pretty impressive. It is also nice to see someone reworking a story even after it is completed. It shows you care about it a lot. I think the story has a lot of potential and I do like the overarching theme.
However, there are a couple things that bothered me and it all pretty much boiled down to the tone of voice being confusing. I'll go into detail about what I mean and which parts made me feel this way. Overall this hampered me being able to connect to the story and the characters. My favourite part was the ending because I felt that the tone of voice suited the message, where as in other parts of the story they seemed more in conflict.
I also usually encourage people not to overdo descriptions in their writing, especially for things like visual novels, but I think you could benefit from it. Hearing a bit more about the character's reaction to the world, sensations and sounds, feelings and emotions, these types of things would have been nice with a bit of elaboration.
I had issues empathising with Tobias. I didn't feel his reactions suited who he was, what his goals where and his beliefs. I am assuming that he isn't sociopathic, so he should be capable to empathising with other people. However, he was able to hang out with Winy while still plotting her murder. The inner turmoil that he should have been having was not as clearly portrayed as it should have been. Murder is quite a big deal. I was expecting to see more stress symptoms.
Which leads me to my next point. I don't really get why he was so driven to kill Winy. I do get what your point was, but I don't think it was driven home enough. It was mentioned that Tobias was tormented because he lacked one wing, but it wasn't mentioned in what way, to what degree, what effect it had or in what circumstance he lost his wing. Winy's story was more touching because we got a little bit of background information. With Tobias I didn't have enough information to see it warranting murder. i think the importance of flight to their species needed to be underlined more and there should have been more exploration and explanation on Tobias emotions in order for the audience to empathise to the point where they could see his rationale.
A case in point is one of my favourite series. In it there is a winged race called Eyrien. One of the main characters is one and the importance of his wings and flight are very well developed in his character and his story. His mother was Eyrien but she was either was born without wings or had them removed. When he was born his father knew what he was and how important his wings would be to him. His mother wanted to cut off his wings so he could be brought up pretending to be one of the more privileged races. His father forbade it, threatening to kill the baby if she cut off his wings. He knew that if the child grew up without his wings he would always be longing for the sky and wondering why. Later, when he is grown up, he says that he would rather lose his balls then his wings. In a part of the story his wings are destroyed by mould and it is a pretty touching part of the books. In this series it is understood how serious the wings are to this particular race. I accepted his father's threat to kill him as an act of kindness rather than cruelty because of that. it would have been very different if the importance of the wings was not understood.
In your story I think I would have understood it more if I had a better understanding of how important his wings were to Tobias. His emotions were very important in determining his actions.I think some added description would have helped me to empathise with the characters, gave me a better understanding of the story and would have slowed down the pacing nicely. As it stands I felt the story wavered from being a serious story that involved plots of murder to a light hearted comedy. Light moments are good, but in this case, especially told from Tobias's perspective, they should have been tinged with more negative emotions (anger, regret, jealousy, guilt, hate, sadness), even if they were just privy to the reader. I think the tone of voice need to be more consistent throughout the story.
Apart from that, most of the technical aspects seemed good (from what I know ^^'). I didn't really like the whole screen blinking when character appeared, but that might just be me.
There were one or two inconsistencies and typos, but nothing major (I'm pretty sure Tobias mentions being 22 right at the beginning and then a couple moments later changes to 23, as well as 'heeding' being spelt 'heading')
Anyway, wonderful job, I did like the story and it is obvious you care very much for these characters. That is always a good sign