What are the basic rules of how light and seasons affect landscape and objects lighting?
I suspect that the answers you seek lie as much in computer graphics and human perception as they do in physics or earth science - for example, colours on a cloudy day won't actually be significantly less saturated than on a sunny one - it's still white light to most intents and purposes - but we may perceive them that way due to the differences in contrast, illuminance, and colour.

There are three components to natural light :

You can calculate the angle of the sun according to time of year, time of day, and latitude. From this angle, and the altitude of your viewpoint, you can estimate the colour of the direct sunlight. The more air it has to travel through, the lower the colour temperature and the intensity. 

Then you need to consider the blue sky. This will be lighter at low altitude and darker at high. You'll need to do something about the sunwards sky not being blue at low sun angles. The blue sky casts light on things, but this is mostly only evident by shadows appearing a bit bluer than their surrounds.

Then you need to consider cloud cover. For a flight sim this is complicated by the fact that it may be above or below the camera, or you might be in it. One approach might be to treat clouds as large diffusers that act on the light from the sun and from the blue sky. Whether this is feasible is beyond my ken, and definitely lies in the realm of computer graphics, not earth science.