I will preface this response by saying I know I am weird. 
The difference for me is in how I am playing. I tend to RP all games, be they IF or video games. I literally have entire head canon stories for every game I play, including games like Fallout or Skyrim, because open world games tend to be so shallow with character interactions. In games where the character interaction is more satisfying, I’m less likely to do that as deeply, but I still do it. I also spend ungodly amounts of time on the character creation screens, with me trying to figure out just who the hell I’m about to RP.
In IF, I do the same thing. There are several reasons that second person makes it more difficult for me to connect with the PC well enough to “figure them out”. One thing is that I don’t self-insert, and the “you do this” tends to jerk me out of “character” so to speak, and get me in a mindset where I’m just, proverbially speaking, shoving a piece around the board.
It’s like… verbal chess, where I’m “controlling” a single piece to some extent and the author not only controls everything else on the board, they’re also constantly telling me where to put my piece. I can’t connect with a pawn on someone else’s board, especially when I feel like it’s not even my piece.
I’m not sure if this makes any sense to you, but I suppose it feels more… hollow? Like the difference between reading a history book about nameless faceless people you never met, don’t know, and don’t really give a damn about and reading a more personal account of the same topic, where you can attempt to step into their shoes and experience their story with them.
IF that is written in first person feels more like the latter to me, and I think maybe it’s because I don’t have to make so many “jumps” in my head to get that connection. With a first person IF, I can “create” my MC for the story, then get into their headspace and feel my way around the story to figure them out. It makes it easier to deepen the character in my head, too, to fill in the blanks that are left by the author and narrative.
It also makes it easier for me to make decisions, because I’m making them as that character. When I say I RP these games, I mean it literally. The “I” is the character. When the story keeps using “you”, my brain immediately goes to me, not my character, so I have to either stop and think before making a choice, code dive and just pick the path I want for the my character to get, or I end up just picking crap on a whim, and it breaks whatever MC I had in mind, pissing me off on the process.
As for the “why”, the narration doesn’t always provide it. In fact, it typically doesn’t give a good reason for doing ‘x’ even when it does provide a reason. Or it’s a reason I have trouble identifying with, which is just as bad. In an “I” story, my character can somewhat work around that (or ignore it altogether and do it for her own damned reasons). In a “you” story, I am once again left sitting there sneering at the screen because I either find the reason we’re given to be incomprehensible or feel even more of a disconnect with the MC and the story. With “I”, my MC can fudge it for me.
For me in Wayhaven, my MCs just ignore that crap and have their own, more appropriate, thoughts. If it was second person, I think I would scream, because there’s no way in hell I could identify with that pathetic tween whiner who’s incapable of doing a damned thing without falling apart.
For writing, I prefer third person. Writing in second person is horrible for me. I feel like I’m a drill sergeant forcing all the characters around on a board and lose any emotional connection I have with them.
Most of what I read is third person. I’ve read some in first person. When it’s done well, I like it, but it’s rarely done well. I can’t recall ever reading a book that was written in second person. Unless you count instruction manuals with an implied “you”. Or instructions I write for users that do include “you” where appropriate.
