First of all i want to commend you on finishing this game, its a hard thing to do and well done.
Secondly, I'm sorry if i come across as harsh in my following critique. I only mean the best in listing things that could be improved.
1) It takes entirely too long for the player to make a choice. You're going to lose players if you don't engage them early. A good way to engage the player early would be to let them chose some basic customization options, say their name or their gender.
2) The first choice's options should feel different. You can have choices that are all effectively the same like that but it should not be the first choice. That combined with the long times between choices makes the player feel like they are reading a book instead of playing a game.
3) I personally couldn't really follow the story. Though this could be a problem with my reading comprehension.