Reading it on a screen with these dull minded annotations? I'd hate for this to be anyone's first experience of it...
Is scandox making an assertion here? Could be, or perhaps it's a just a meager judgement. Whether or not he/she really thinks this is a pleasant first experience is open to question.
What you may need is something like reversing the direction of the links. That is: A footnote is a link from the main text to the note. The links (or the indications of the links) clutter up the main text, breaking the flow (or at least inviting you to do so). For a normal text with a few footnotes, that's probably the right approach. But for a story with annotations, maybe the right answer is to have the annotations have links to the text. That way, you can just read the clean, unannotated story. Or you can read the annotations and see the story text that they refer to.
An alternate approach would be to have a switch, where you could turn off the display of the annotations.