For the first half of Pupetter I thought the story was overbearing. Each level begins and ends with lengthy exposition and the Narrator constantly quips semi-witty one-liners while you play. On top of that, I thought there was too much happening on screen - too many bright, moving pieces to keep track of, each beautiful but creating chaos rather than one coherent image which drew my eyes from each important object to the next.
My brain could only handle one thing at a time; play, listen, or look. As such, I missed a lot. To mitigate this problem, I'd stop moving when the narrator spoke. That worked for a while, but eventually slowed down the pace of the game so much it became boring.
A friend of mine who watched me play some of the game's later levels had the same problem. I'd catch him out of the corner of my eye vigorously blinking and shaking his head and shortly thereafter hear him say something like, "What the fuck is going on? This game is so disorienting."
If you are like us and have/had this problem, I have no active solution for you. Eventually, after about half - or maybe even two thirds - of the game my brain acclimated to Puppeteer's deluge of sensory stimulus. I could lie back and, in what felt almost like some drug-induced/meditative state, soak everything up all at once. If I have any advice, it's don't try to make the game intelligible; just let it happen. Eventually, you'll figure it out.