For a Phalcon oriented approach, a developer would need to know the code structure, the request, and the way the data is stored.
You can reduce model overheads when you bypass the model and work closer to PDO. It only makes a significant difference for some types of access. Think of a list where you want the first 20 rows. The model might read them one row at a time. A direct SQL request could ask for 20 rows at a time, reducing the internal processing.
When you change the model usage, you can see some of the effect through request logs. If your request translates to SQL, some databases log the SQL request and you can use the log to pick up some perfornace problems. You could then as a specific question here. You could post the generated SQL and ask how to change the model to produce bettwer SQL requests or how to change the model to produce better indexes on the tables.
I contributed performance enhancements to Drupal in the form of SQL and table structure changes. That was achieved by looking at the SQL log.