(first time commenting)
As a developer using "game" web frameworks, I feel you're not wrong but you just missed an important point. Boilerplates are mostly used for learning and as reference rather than as a boilerplate that you'll effectively use. Yes they often are over-engi eered, I agree with you. But I deeply think that's not the point. To learn, they are perfect. To use, no. As a learning reference, yes. As a core architecture, that's risky.
And I won't even discuss about whether to use phaser over pixi/unity/any other framework. (ok my heart goes to pixi/howler without doubt over phaser) (that's between us)