This also applies to indoor photography in general: stop using flash.
A layout with marvelous scenicing, detailing, and weathering turns to instant messy cartoon look under the harsh glare of a flash. Set your camera so the flash is forcibly turned off.
If you can, get your layout close to a window and use the natural outdoor light to illuminate it ... or if it's small and lightweight enough, just take it outside! I've actually found that bright overcast days give better results than sunshine, because there are fewer harsh shadows.
If there's no way to get natural outdoor light near your layout, the next best method is to find a powerful incandescent light and get it close. Make sure the white balance on your camera is set to incandescent. Observe the shadows and the "tone" of the light very closely and feel free to adjust the light position before you press the shutter.
Finally, either in your camera or using photo software, experiment both with increasing the contrast and decreasing the color saturation. A little of each goes a long way.