Indexes on XtraDB tables
You should index as per usage. If you drop all indexes for the benefit of a small % of your workload you will hit pain elsewhere. Run pt-duplicate-key-checker 1st and remove the redundant keys. Then review your queries with pt-query-digest and weed out the poorly performing queries by reindexing them or rewriting them. You could paste the output of EXPLAIN with your table structure and status for your problematic query for further help tuning on that.