What is the problem you are seeing? Dirt? Mud? Yes, chickens tend to create dirty surfaces, and as they are in no way harmed by some degree of it and you'd have to keep after it daily if you want your coop to look like Martha Stewart's living room, yeah, most peoples' coops are "outdoor livestock" looking rather than "operating room" looking. Although, the nestbox in the third photo could definitely use cleaning out.
As far as mud, note that he has ducks so it's worse than it'd necessarily have to be with chickens; but even with just chickens you are NOT going to be able to keep grass in your run unless it is huge or rotated regularly (and even in those cases, it tends to go to bare earth -> mud right around the popdoor) so either you have to put some other footing in there or live with dirt/mud. Some of the things people put into the run to deal with mud can actually make a worse problem in the long run; see my 'muddy run' page (link in .sig below) for further discussion of subject.
They're chickens. They're outdoor creatures. They walk around barefoot in the dirt all day, including stomping happily thru their own poo if it happens to be in the way. They drink from dirty puddles. They poo on everything. They are dusty. Just because you yourself would prefer not to eat off a particular surface does not necessarily mean it is unhygeinic for outdoor animals to eat off or walk around on. (Of course there is a line between normal 'outdoor dirty/messy' and actual unhygeinic filth, you would avoid the latter, but your b-i-l's setup is not even remotely approaching it)
If you want all surfaces to be spotless bright shiny white, or golf-course grassy, chickens may be stressful
OTOH if you are ok with them being normal critters rather than magazine photo spreads, it may be just a matter of adjusting your eye and getting used to it
Good luck, have fun,
Pat