It's been suggested in the past. It means making layers into a tree structure. It would be great, but would also be a complex and time consuming feature to implement. As with all feature requests, we're a small team with limited resources, so we have to carefully prioritise what we do. There's several years of feature requests already filed on the suggestions platform.
I understand. If we do not take in consideration the grouping layer, it would be possible just to disable any effect applied to a specific object or layer? This would solve the problem anyway. Like a toggle options or a behavior that says "do not apply any effect".
For instance, I have a sprite that makes all the hud graphics.In the layout effect, I use the effect to make the level looks like really dark changing the contrast, brightest and the colors. I could achieve the same effect by changing the textures of the game (and then apply the effect to sprites I need), and that actually would work saving some GPU (maybe). However, I use a dynamic light, meaning that depending on where the player goes, the light change according (like if the player goes into the cavern in real time, all the lighting and color changes smoothly). As you would imagine, if I apply the layout effect, the HUD will get affected by it. If I have an option to disable the effect to a specific layer or sprite, then we wouldn't need the grouping layer. Also, changing the texture in this case would be really hard to do it (adding more layers, changing opacity...etc. So effect would be the best and easy solution I guess.
PS: I see that you are working on the scene graphs and that is great (it is also sound really complicated), however I think that the grouping layer is something more helpful for a vast majority of people and should be a core options on construct 3. But I understand how difficult would be implement this feature.
PS2: is there any JS script that would allow to disable the effects to the specific instance even if the effect is applied to the layout?