Thank you so much for such a detailed comment, I appreciate the time and care that went into it! And no worries, the easter eggs were hidden very well on purpose-most people never find them on their own so you're not alone! I can give you a hint if you want :)
And I know what you mean about the continuity, I got the same feeling from reading comics sometimes! Like having the main character acknowledge it makes it more official, it was fun working that into this game-and haha so glad the deaths are making you think hard!!! Those are so fun to write and draw for, and I'm glad they're having such an impact! No need to restart, the flowers are fine-but glad you noticed that detail, it sets the stage for the Forest and what it's like in there!
Speaking of which, I'm so glad you're paying attention to all the story details in general! And yes, the fourth game is actually coming out in just a couple weeks! Forgive the plug, but you can stay updated on what I'm working on if you follow my twitter or tumblr XD (You can also just swing by to chat, I enjoy talking to my players^^)
And sort of? The ending has to do with a very important sub plot that will be explained not all at once, but piece by piece as the story unravels throughout the games! So it will make a little more sense in the fourth game but you'll still have plenty of questions unanswered >:3c