In this case, the "bubble" is the thing...but yeah, it's a little noisy. Perhaps if we fuzzed out the background a bit when the annotation viewer (the bubble) is open it would help?
Please don't do this. It was immediately obvious to me which part was the part I was supposed to read. (And I've never visited this site before today!)
I personally managed to follow the series without difficulty, though I can sympathize with the parent's sentiment because I felt a brief moment of confusion when the page first loaded. Excellent write up though! Looking forward to going through the rest of the content after work today.
I'm no UX expert, but I think if you want story reading to be a core feature of your product it will have to have a core place in your layout, so not a pop up box. It would replace whatever currently is your main feature (I.e it would become the left bar).
I think the thing to do might be to detect if the page was loaded with the annotation open, then fuzz background. Otherwise, you know what you're looking at and explicitly clicked the open annotation button.
It's great that the site supports such deep linking.
My original comment was worded poorly. Left side blur should be on initial load if the referring url is not from the same site, not every time you open an annotation.