Simply put, because the reparo spell can't renovate faded materials or make poorer wizards wealthier.
@Janus Bahs Jacquet made this point well. You could 'fix' a rip in some robes using reparo but this wouldn't do anything to renovate, improve or increase the longevity of older items. However, I think the crux of the question is less to do with reparo and more to do with the role of wealth in the wizarding world.
In relation to Lupin, the condition of his robes has a clear role in the story: to underscore how poor he is. Let's recap what we know about Lupin's robes.
The stranger was wearing an extremely shabby set of wizard's robes which had been darned in several places. He looked ill and exhausted. (Prisoner of Azkaban, Chapter 5, The Dementor)
Lupin has less money to spend on robes and the like because of his identity as a werewolf:
"Dumbledore's trust has meant everything to me. He let me into Hogwarts as a boy, and he gave me a job, when I have been shunned all my adult life, unable to find paid work because of what I am." (Prisoner of Azkaban, Chapter 18, Moony, Wormtail, Padfoot and Prongs)
This point is underscored when Lupin's appearance is compared with that of the other teachers.
Professor Lupin looked particularly shabby next to all the other teachers in their best robes. (Prisoner of Azkaban, Chapter 5, The Dementor)
I think we can safely say that Lupin's robes were shabbier because he has led a life of exclusion and forced poverty in comparison to the (presumably) well-paid life of a Hogwarts teacher. It isn't that Lupin simply isn't as good as the others at performing reparo.
Firstly, then, Lupin's robes tell us something about his wealth status.
Additionally, I think his relative poverty says something when compared to his predecessor as Defence Against the Dark Arts teacher.
Gilderoy Lockhart, however, was immaculate in sweeping robes of turquoise, his golden hair shining under a perfectly positioned turquoise hat with gold trimming. (Chamber of Secrets, Chapter 6, Gilderoy Lockhart)
Out-of-universe, this seems to be a point that Rowling likes to make about her characters. Lockhart was always immaculately presented and yet turned out to be something of an idiot. Likewise, the Dursleys care deeply about how other people perceive them as a family and yet are cruel and callous behind closed doors. Lupin's appearance reflects well upon him as a character. He may seem scruffy at first but turns out to be a very trustworthy, loyal and sacrificial person in the course of the series.
In-universe, it seems likely that Lupin would much rather spend whatever gold he has on random magical creatures like Grindylows rather than on robes, haircare products and the like.
Secondly, then, Lupin doesn't care much about his robes and that reflects well on him as a character.
Finally, to return to the point about reparo. It can't change the fundamental nature of something, only return a substance to its original state. We see this most clearly with Ron's dress robes. They're described like this:
He was holding up something that looked to Harry like a long, maroon velvet dress. It had a mouldy-looking lace frill at the collar and matching lace cuffs. (Goblet of Fire, Chapter 10, Mayhem at the Ministry)
The robes are just plain nasty. Later Ron successfully cuts the lace off with a Severing Charm. However, he can't help that his robes suck. The robes aren't broken, just manky, so reparo would get him nowhere.
Thirdly, then, reparo can fix broken things but can't undo tatty-ness.
Once again, this comes down to wealth.
"Well, they're OK!" said Ron angrily, looking at Harry's robes. "Why couldn't I have some like that?"
"Because...well, I had to get yours second-hand, and there wasn't a lot of choice!", said Mrs Weasley, flushing. (Goblet of Fire, Chapter 10, Mayhem at the Ministry)
The reason Ron and Lupin have scruffy, worn-out clothing is because they are poor.