Just because it is easy to cast a spell and clean up or make repairs doesn't mean every witch or wizard will have the time, or be motivated to.
Just like Muggles, wizarding families produce the lazy and slovenly. Mundungus Fletcher, for example, is not someone I could see diligently checking his roof to repair broken shingles.
Others, such as Xenophilius Lovegood fall into the category of "eccentric", even by wizarding standards. While that's not to say his house was in disrepair, wouldn't it seem plausible that something as mundane as peeling paint might go unnoticed by him for weeks, if not months?
Still others may have simply chosen "run down" as a stylistic choice. The Blacks, for example, seem to enjoy the "old and dark" aesthetic.
As for the Weasleys, well, they're just busy. With 6 kids (or is it 7?), and Mr. Weasley working hard at the Ministry of Magic, there is only so much time to take care of odds and ends. Even magically assisted chores take time, and chores for a large, active household add up (let's not forget that they don't have a family house elf; that seems reserved for the wealthy wizarding families). Foods that cut themselves up and jump into the pot still take time to cook. Clothes still need to be sorted for washing and mending. Given their focus on "functional and practical" (remember Ron's hand-me-down formal robes), is it any surprise that "intact and working, if a bit banged up" is an acceptable standard for their family home?