People can play the mindless "coach started him therefore there's no doubt player was better". That thought has been proven wrong multiple times outside of ND.
Within ND, no one will ever convince me that Joe Schmidt should have played every snap over Nyles Morgan his senior year... that K Met didn't deserve Alize Mack's snaps when K Met was healthy... Or that Dexter Williams shouldn't have gotten ~12 carries a game as a Junior.... did you know he would have set the NCAA record for YPC, but he was like 2 carries short of qualifying?
Jokes.
While there have been occasions when the coaches have played the wrong player, more often than not they've gotten it right. Just looking at the QB swaps they've tried under Kelly:
2011 Crist got the start over Rees, and from day 1 this was the only one they most certainly got wrong. Rees was the better player in 2011, he took over during the South Florida game and never really looked back. When Rees got injured for part of the USC game they had to put Crist back in and it ended badly. Crist never bounced back from his injury, and he unceremoniously finished his career with Weis in Kansas.
2012 Golson was the guy, but there were some times he struggled. While Tommy did bail us out during a few games, they tried to pull Golson during the Pitt debacle and Tommy struggled even more than Golson. Golson was definitely the guy in 2012, coaches started him over Rees and it was the right move.
2013 Rees was starter again after the Golson suspension. They tried to pull him for Andrew Hendrix and it once again ended badly. On one particular occasion during the USC game Tommy suffered a concussion and the coaches were forced to put Hendrix in to finish the game. I don't think Hendrix got a first down the entire 2nd half, we won that game strictly on the points Rees scored the first half. Rees was the starter, and he was clearly the best QB on the roster that season.
2014 Golson was starter again, but he lost his mojo late in the season. Zaire got the start for the LSU bowl and was voted the MVP, but Golson still saw plenty of action and was shown to be the better passer. Mixed results here, but Golson was certainly the right guy to start the year before he collapsed. That Michigan game was beautiful.
2015 is a bit of a bust, Kelly was forced to start Kizer and change the offense after Zaire breaks his leg, but based on Kizer's immense struggles with the offense in the Blue Gold game they started the right guy at the beginning of the season.
2016 Kizer began the season as the starter with a lot of fans clamoring for Zaire's return, but it turned out Malik was never the same after the injury and the offense no longer had a strong run game which severely hindered his skill set. Coaches made the right call again by starting Kizer.
2017 Much like 2014, Wimbush got the start for most of the season without controversy. Wimbush absolutely destroyed USC and NC State, but something may have broken him after that Miami game. After Wimbush struggled against LSU he got pulled for Book, Book led the comeback. Perhaps Wimbush should have been pulled sooner, but we can't know how ready Book was prior to that LSU game. Had they not pulled Wimbush we lose that LSU game though, and we wouldn't have that sweet final TD by Boykin. Given the way he started the season it's hard to say the coaches made the wrong call, something certainly changed in Wimbush after Miami though.
2018 Wimbush got the start again and may have been the right call for the Michigan game for his ability to push the ball downfield, but after struggling against Ball State and Vanderbilt he got pulled in favor of Book. Book was certainly the more complete QB, the staff made the right call at the right time to go in a different direction from Wimbush. Neither QB was going to beat Clemson though. This could arguably have been another time the coaches got the starter wrong at the beginning of the season, but given Book's performance against Michigan in 2019 I think the coaches starting Wimbush against the Wolverines worked out better and was the right call.
2019 Unfortunately Phil was such a question mark and mostly just saw garbage time, so there's no way of really telling how good or bad he really was. What we do know is Book was exceptional down the back half of the season and he played fairly well against a tough Georgia team too. He certainly struggled against Michigan, but that debacle was a team effort that Joe Montana couldn't save. Michigan game aside, Book showed down the stretch how good he really was and it's unlikely Phil would have outperformed him.
So, more often than not the coaches tend to start the right QB at the right time I think. The one or two times they did pull a long time starter in favor of the backup and it worked out it was pulling Crist for Rees and Wimbush for Book. In both cases a highly touted recruit was replaced by a three star prospect that went on to excel. For those reasons I think you can argue maybe those guys should have started sooner, but perhaps the "five star" mentality got in the way and clouded the coach's judgement.
As far as Nyles Morgan, I think people forget that the coaches DID try and insert him into the defense in place of Joe Schmidt and he was clearly not ready. Our protections were wrong, and Nyles was out of position. He was clearly more athletic, but the defense was better as a whole when Joe was in. Who's to say if it was the coach's (Likely VanGorder) fault for failing to prepare Morgan, or if Morgan was the one struggling with the position. Nyles certainly improved his senior season under Elko, they simplified the defense a bit and let them read and react more. 2016 was a different story once Schmidt was gone, but that defense was awful across the board and led to VanGorder getting ousted.