Fast travel between checkpoints was my main idea. The other idea for smaller bits would just be like levers or button or whatever that you can trigger and open up some sort of path to get from A to B faster. Not necessarily something huge but maybe instead of climbing up this ladder type thing you can just take the shortcut up. The movement speed could also be overall faster but I think for this game a faster speed wouldn’t really work well. All in all I think fast travel would fix most of the issues so I’d focus on that and circle back if there’s extra time.
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I really like the manual however I wouldn’t prioritise over the metroidvania elements. I also think collecting them shouldn’t be the win condition, I think it was fine in this case but I’d love some other way to feel a sense of completion.
TLDR: I like the manual and think you should keep it but not focus on it.