I mean I have worked on a Visual Novel idea for a bit with multiple routes, but I haven't used Twine before.
I also didn't get super far, it only took a few days of work and like 10k words for me to realize that the freedom I wanted to give ballooned the scope of the project well beyond what I wanted to do lol.
Even with just three main routes, the branching paths going there was a huge head ache to write it all.
when I was doing this I was messing around with Ren'Py
https://www.renpy.org/why.html
I was also messing around with TyranoBiulder
http://store.steampowered.com/app/345370/TyranoBuilder_Visual_Novel_Studio/
both of which would let me do the story without to much needed coding, would just need to insert the text, and direct where the pages go and eventually add art.
Don't know if any of that helps at all though ^^;