It is true that including PHP files is faster than querying an SQL database, but you'd have to re-write a lot of code for one little change. The advantage of SQL databases is querying. You can select only the values you want, however you want, while flat files require you to write functions to deal with that. SQL saves you a lot of coding because the functionality is already there, no need to write extra code.
If you wanted a completely optimized fast-as-lightning application, you would use flat files. But then again, if you were really that worried about speed, you wouldn't be using PHP, you'd be writing your own application in C. Trust me, no one is that worried about speed.
The optimal storage method would be an SQL database with PHP files to cache stuff.