PHP framework building: System Class (reads configuration .ini file)
Some improvements(they would save your[and framework users] a lot of time on debug):


All system wide components should implement pattern Singleton, this would guarantee that you have only one System at the same period.
Try to create interface SystemInterface, this would allow you to create ServiceStub pattern(It's very useful on testing)
Split your class and move parser to another class(use Strategy pattern). Your system should depend on configuration, not file! Also this would allow you to create another config-files like .json or even .php
Configuration shouldn't be stored in applications main class, use ConfigurationRegistry for this(pattern Registry)