Aaron Jorbin created a script to download every theme from the WordPress theme repository, and Devin Price has used the script to slurp some interesting data from those themes.
For instance, he guesses that ~17% of themes utilize Underscores as a starter theme, and that around 24% of themes use the customizer.
He also backs the data with his methodology for estimating. It’s a great read, and I’d love to see more experiments with this data.