Wow, thanks for playing again!!!! :) :) :)
You're really good at finding the not-so polished and added-later things. :D But this is exactly the feedback I'm looking for!
There are a few levels that branch out a bit but you're right, this is not very prevalent yet and could be improved.
About the upgrades: you can actually re-distribute the upgrade points at any time. Looks like that's badly (or not at all) communicated. Some of the upgrades are rather gradual like the movement and jump speed. I understand you felt underwhelmed by their effect. These are more meant for doing high-speed re-runs to beat challenges and such. Just handing all these upgrade options to the player is probably a bad design decision. I'm currently thinking about only unlocking upgrades bit by bit as well as grouping them into categories (speed/survivability/etc.). Maybe hiding them behind optional paths would make them even more meaningful as well. And requiring a number of shards for unlocking these optional paths on the world map. You gave me lots of inspiration! :)
Unskippable cutscene: yeah, that's just bad! Sorry, I didn't have the time yet to implement a proper fast-lane if you've already seen the cutscene.