You are referring to the green of the tree, not the trunk, right? This does not have anything to do with the lights branch, since the trees already look this way when the are overground, and I think they looked just the same before the lights branch was merged.

I think the problem with this simply is that we have only one directional light from the front, and so triangles that are perpendicular to it are very dark. This makes sense for most objects, I guess, but for trees it's a bit funny because one triangle represents a lot of leaves that, in reality, would be all oriented in different angles with respect to the viewer.

For overground objects, we could go away from using a directional light and instead just illuminate the whole object uniformly. However, this would change the appearance of several objects considerably, and things would look much "flatter". We could also make a compromise like 50% uniform and 50% directional... plenty of options, but someone needs to play around a bit and see what looks good. All these settings are changeable without engine changes by editing the shader code in Graphics.ocg/*.glsl, so I encourage you and others to play around a bit :)