In Prisoner of Azkaban, Hermione took 12 subjects, and needed a Time-Turner to do so. However, it is mentioned in the series that both Bill and Percy Weasley got 12 OWLs, so would have taken 12 subjects as well, so both would have needed Time-Turners for three years to do this. Doesn't this seem a little unusual, given how strict the Ministry is over the use of Time-Turners, that they would give them to several Hogwarts students?
Hermione seems to have needed the time-turner primarily because she had four lessons that conflicted with each other; (Care of Magic Creatures/Arithmancy, Muggle Studies/Divination).
‘Getting to all her classes!’ Ron said. ‘I heard her talking to Professor Vector, that Arithmancy witch, this morning. They were going on about yesterday’s lesson, but Hermione can’t’ve been there, because she was with us in Care of Magical Creatures! And Ernie McMillan told me she’s never missed a Muggle Studies class, but half of them are at the same time as Divination, and she’s never missed one of them, either!’
The most likely, and sadly most mundane explanation would be that in previous years the lesson planning simply didn't result in any overlaps, negating the need for a time-turner and allowing high achievers to attend all twelve lessons.
It's important to remember how Hermione managed to get her time-turner, because it's not easy:
'It's called a Time-Turner,' Hermione whispered, 'and I got it from Professor McGonagall on our first day back. I've been using it all year to get to all my lessons. McGonagall made me swear I wouldn't tell anyone. She had to write all sorts of letters to the Ministry of Magic so I could have one. She had to tell them that I was a model student, and that I'd never, ever use it for anything except my studies'
From PoA chapter 21, "Hermione's Secret".
It's also important to remember that Time-Turners appear to be under the control of the Department of Mysteries - we see a room full of them get smashed to bits in Order of the Phoenix, and we're told later in the series (No quote because I don't remember exactly when) that every time-turner was destroyed in that incident.
Given the extreme secrecy of the Department of Mysteries1, the fact that McGonagall even knows that this is a thing she can do indicates that she's done it before, or that there's some precedent for giving them to exceptional students2.
Speaking of exceptional students, there's a pretty finite list of people I would imagine as even being under consideration for this special privilege. Hermione is obviously one, especially in the earlier books, honest-to-a-fault as she is.
Percy, meanwhile, is consistently portrayed as a nose-to-the-grindstone kind of guy, who follows rules and expectations almost compulsively.
Bill, on the other hand, is the role model for the entire Weasley family. We don't learn terribly much about his character, but his accomplishments are quite impressive. What's also impressive is the fact that nobody really seems to dislike Bill, or feel any negativity towards him whatsoever. He is, essentially, perfect.
It's also significant that both Bill and Percy were prefects and Head Boy in their respective years. I think the only other person confirmed to have accomplished that was Lily Potter.
Short version: Bill and Percy are the kind of elite, A+++ students who you would expect be allowed to qualify for a time-turner if they needed one. Of course, as Richard points out in a comment to the question, it's possible they wouldn't have needed one; we don't know much about Hogwarts' class scheduling, but it's not impossible that all twelve of the classes could have been offered at non-overlapping times.
1 You might say that they're...mysterious
2 Granted, it might also just mean that she knows the Plot-Advancement spell, but that's a boring answer