I’ve noticed recently using the various MySQL command line tools that many WordPress related queries are *very* inefficient because many of them are doing full table scans.
Most of the time full table scans can be avoided by using indexes on the fields that are part of the “WHERE” portion of an SQL statement.
With that being said, I must say the biggest problem is probably all the plugins written by people who don’t understand how to properly create database schemas that are optimized for the type of queries that will be made on the tables.
I’d love to see some more effort being put into making sure all plugins and even base WordPress SQL tables use indexes properly so that the number of full table scans are reduced.