You fail to mention if you use any kind of caching in your benchmarks. Assuming you don't, the easiest way to improve your performance is to use a byte code cache for your code and query/memory -caching for your database.

Another good practice is to manualy add the include/require statement to files instead of relying entirely on autoload to do the job for you. (I know this one is hard since autoload is sweet like the nectar of ambrosia) Although this is only useful if the included code is always used by the code in the file. (In which case you should use require_once anyway). A good example of when this practice should be used is class inheritance.

Even with a byte code cache the framework will add some overhead due to its file structure. If further performance improvement is required one way (although tricky) of squeezing some extra performance out of your site would be to write an application that would replace any include/require statement with the actual code to be included where ever possible. One would have to take care not to include the same file more than once tho.

Note that you would run this program on your code before you uploaded it to your live server. This way you would have the benefit of code separation while working on the code and the benefit of not having to parse multiple files when serving pages to your audience.

Before you ask, no I haven't actually done this (the include replacing app that is) myself. But I have read that some of the big fish out there in the world do this.

Hope this helps.