Let me introduce you to the Phaser Goldilocks Template. It combines everything I wanted during that first week of Phaser. This solves a few things. First, for development all code can be separated into different JS files. For production, all JS files can be combined into a single one for the fastest loading. The second thing this solves is the common scoping pitfalls I see many people encounter. So no need to use prototype as the game variable is available in each file.
https://github.com/EddieOne/phaser-goldilocks-template