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Oh my gosh I've been so busy with stuff I haven't  seen this question!
To answer the differences, the story has been completely redone and extended, same goes with  the dungeons and areas you explore, You go back and forth between Gensokyo and Mitakihara. Gensokyo being more of a chill side story section while Mitakihara is the RPG battling section.  

Once again I'm sorry I didn't see this sooner! I'm surprised to see someone who's played the OG game here (I'm a little embarrassed of it now honestly...) But I hope you will be interested enough when it releases in a  few months!

I really should've made a mention that you can save in the pause menu and asked the game if you want to save before starting the first labyrinth.  I apologize!