The PoWA project (https://dalibo.github.io/powa/) + pg_qualstats extension is doing most of this work.

The pg_qualstats extension will gather statistics on WHERE clauses (number of execution, selectivity...) on the fly, and the powa UI can show you which are the most expensive queries, and suggest index creation based on your real workload. It's then your choice to create the indexes.

hypopg should be added soon to compare query EXPLAIN with and without the hypothetical indexes.