From what I read and observed, this is one of the reasons for using a scatter plot: to see where the datasets overlap, group together and show a possible correlation (see the formal definition in Wikipedia: https://en.wikipedia.org/wiki / Scatter_plot ).
You might want to add a note to the chart that encourages your users to zoom in to see more details. The zoom feature is a native part of Highcharts / Highstock, but is not immediately obvious to many users.
It is worth noting that you can limit the scaling to one axis ( zoomType: 'x' ) or both axes ( zoomType: 'xy' ); see http://api.highcharts.com/highcharts#chart.zoomType . This may offer you a little more control over how you want your users to view chart details with lots of overlapping dots.
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