I think there are some misconceptions in what you say and I will try to explain why and what is the philosophy behind this specific game which is a bit peculiar too.
First of all, I personally don't like how Ren'py behaves by default and if you mostly play Ren'py game, this is what you are used to so you probably don't think much of it but the default of Ren'py is absolutely not the standard in general.
For example, the way you can resize the Ren'py window like a chewing gum/web browser is an exception in video games, it is the default behavior of a program if you don't do anything to it, it's not actually something that is 'designed' and it's not good for multiple reasons that can differ depending on games, but in general it looks bad and cheap because you can never end up with a properly shaped window, it will always have some black bars in some areas because it's not humanly possible to pixel perfect by hand a window. The second problem is that it makes it difficult to return to the native resolution of the game (the resolution where the pixels are at 1:1 scale without deformation), there are tricks to do it in default Ren'py but not everyone is aware of it.
It looks unprofessional in my opinion and this game is trying to reach beyond Ren'py gamers, like most of the screenshots shared on a Ren'py game will have those weird distorted windows/maximized windows like it's some kind of web browser application (again this is the default behavior of a program in general but for a game you want to avoid that imo).
With the resolution selection, I'm mostly inspired by Japanese VN and others game and their way of doing things with fixed windows, I do plan to expand on it by adding a lot more resolutions to cover all the needs in the future so you will have the same level of customization to have it at the size you want while avoiding ending up with those weird windows that base Ren'py tend to have.
This also works much better with the retro feel of the game, this is a design decision for this specific game because the not modern feel goes with the retro fantasy, but for example on a modern side project, I'll keep the default chewing gum feel of Ren'py because it's less of a game, and more of a short trashy game than anything, addressed to Ren'py classic vn crowd.
For your second point, this is already corrected in R9.5 if I understand right, the windows recenter from the middle now. This is something that I wanted to improve from some versions now and did with the last SDK update.
About skip, wrong, it's not auto-forward, this is Skip as you know it just works through a toggle button (supported by Ren'py, not something I created really), which makes much more sense for a sort of point-and-click sandbox game, because you can just toggle it, and playthrough the content without constantly pushing the ctrl button. I don't think there is an issue with it, it works well in this situation.
First of all, I personally don't like how Ren'py behaves by default and if you mostly play Ren'py game, this is what you are used to so you probably don't think much of it but the default of Ren'py is absolutely not the standard in general.
For example, the way you can resize the Ren'py window like a chewing gum/web browser is an exception in video games, it is the default behavior of a program if you don't do anything to it, it's not actually something that is 'designed' and it's not good for multiple reasons that can differ depending on games, but in general it looks bad and cheap because you can never end up with a properly shaped window, it will always have some black bars in some areas because it's not humanly possible to pixel perfect by hand a window. The second problem is that it makes it difficult to return to the native resolution of the game (the resolution where the pixels are at 1:1 scale without deformation), there are tricks to do it in default Ren'py but not everyone is aware of it.
It looks unprofessional in my opinion and this game is trying to reach beyond Ren'py gamers, like most of the screenshots shared on a Ren'py game will have those weird distorted windows/maximized windows like it's some kind of web browser application (again this is the default behavior of a program in general but for a game you want to avoid that imo).
With the resolution selection, I'm mostly inspired by Japanese VN and others game and their way of doing things with fixed windows, I do plan to expand on it by adding a lot more resolutions to cover all the needs in the future so you will have the same level of customization to have it at the size you want while avoiding ending up with those weird windows that base Ren'py tend to have.
This also works much better with the retro feel of the game, this is a design decision for this specific game because the not modern feel goes with the retro fantasy, but for example on a modern side project, I'll keep the default chewing gum feel of Ren'py because it's less of a game, and more of a short trashy game than anything, addressed to Ren'py classic vn crowd.
For your second point, this is already corrected in R9.5 if I understand right, the windows recenter from the middle now. This is something that I wanted to improve from some versions now and did with the last SDK update.
About skip, wrong, it's not auto-forward, this is Skip as you know it just works through a toggle button (supported by Ren'py, not something I created really), which makes much more sense for a sort of point-and-click sandbox game, because you can just toggle it, and playthrough the content without constantly pushing the ctrl button. I don't think there is an issue with it, it works well in this situation.