Thank you so much for the kind words and above all taking the time to download a play through. You've hit on an internal debate I had, had through the initial development in terms of offer player choices. I initially as you rightly observed went for a linear path, similar to VN's like Steins Gate. I am open to change to a more choice based approach as the story develops however, it's really not a lot of extra coding/redering, I just don't want to do it half arsed. Chapter 3 is still very much linear, I'm in the middle of developing Chap 4 (when they eventually get themselves off to Uni :)) and have a few ideas regarding choices, I'm very much leaning towards that approach.
I would totally recommend playing both routes if you have the time, there are different scenes unique to both characters and give you a little more insight into the supporting characters too.
Once again thank you so much for the feedback, you've certainly pushed me further down a course that I agree with you will enhance the story, as long as I can do justice to it.
Edit: Forgot to answer your question on Jon's girls. I have love interests planned for both characters, you'll meet some in Chapter 3 and a lot more in Chapter 4, that's all I can tell you right now :)