I think I know what you mean. KSP has never been about graphics (at least, not to me). Some of the best games ever produced have graphics that could never be described as "eye candy". But at the same time, some of the grandest and most awe-inspiring sights I have seen in a game are from Kerbal Space Program; that view of the sun appearing just over the horizon on your first orbit, your first glimpse of another planet as you are working out a correction burn during an interplanetary manoeuvre, looking up at the majestic might of Jool ominously hanging over you from the surface of Laythe... those moments are unforgettable, even with the limited graphics available in stock KSP. I do appreciate that improved graphics can give an even greater impact in some situations.
Clouds also bring an interesting challenge to gameplay; blocking sunlight to solar panels, obstructing the view of the ground when coming in for a landing, the fear of dropping out from a thick cloud layer and slamming into the side of a mountain etc. These are very cool gameplay/realism elements that clouds can offer, so it's not only about how they look.