I am trying to setup a script that would test performance of queries on a development mysql server. Here are more details:
Full text queries on InnoDB are slow(LIKE "%query%" statements) , there is nothing that you can do to optimize them. Solutions vary from passing that particular table you are querying to MyISAM so you can create fulltext indexes (which innoDB does not support), to denormalizing the row into searchable indexes (not recommended), Doctrine ORM provides an easy example of how to archieve this : http://www.doctrine-project.org/documentation/manual/1_1/nl/behaviors:core-behaviors:searchable The "proper" solution to your problem would be to index the information youre using full text searches on, with a solution like Sphinx Search or Apache Solr.
Like previously said, you must consider the cache state when comparing results, a primed cache gives extremely performant queries. You should consider the cache hit percentage of a particular query, even if it is an expensive query, if it has a 99% cache hit ratio, the average performance will be very high.
Finegrained tuning of queries is not a silver bullet, you might be adding complexity to your application for the sake of optimizations that overall in a production enviroment, are negligible.
Consider your workload, troubleshoot frequent , unperforming queries (use the slow_query_log in mysql, dont blindly start optimizing queries).