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Sphinx has more and in my opinion better themes (especially the popular Furo them). I also think it's better for handling large and complex sites. It's way more extensible. That there are far more Sphinx users means that you're more likely to have community support if/when you run into issues.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.