For those who think that Naruto, Sakura, and Sasuke were unaware of Kakashi's negligent and apathetic leadership - they weren't. Kakashi's bad leadership bothered them quite a bit, something they made evident in their behavior towards their sensei. Naruto, Sakura, and Sasuke didn't much appreciate Kakashi's leadership. While Naruto and Sakura are too nice and forgiving to feel very bitter towards Kakashi and didn't hold his faults against him, Sasuke isn't.

Sasuke's desertion and betrayal will always be the most painful blow that shattered the team, but Kakashi contributed some sizeable blows to the team's unity himself. Many Naruto fans act like Kakashi doing nothing is not harmful, but doing nothing can sometimes be one of the most harmful things you can do, a theme films like A Grave of Fireflies or A Silent Voice are centered upon. Even Naruto explores this concept directly in the Book of Sunrise arc:

"To a victim, their assailant and the bystander who does nothing are no different. That bystander would be no better than the assailant if they didn't try to help. So if you just stand there, pitying the loser but doing nothing to stop the decadence of these rich snobs, well then, Sasuke, you're just as guilty as they are."

Sometimes, when responsibility and obligations are shirked and bad things are allowed to happen without anyone taking action against them, the people on the sidelines passively allowing bad things to continue on their watch are in some ways just as bad as the perpetrators themselves. And this is where Kakashi stands. He shirked his duties, responsibilities, and obligations as sensei and team leader, and his team paid a heavy price for it, culminating in one of them deserting and the rest of them seeking tutelage elsewhere.

There are several instances throughout showing Naruto's and Sakura's displeasure with Kakashi's leadership and teaching:

Naruto's jealousy over Kakashi's student favoritism. Naruto was deeply upset that Kakashi wasn't training him whilst instead favoring Sasuke. This caused serious problems among the team, as Naruto was very jealous for Sasuke receiving blatant favoritism from Kakashi while Naruto was ignored and dumped with a teacher whom Naruto made it abundantly clear he didn't want. This sowed resentment and bitterness between the two boys. Naruto resented both his teacher and his best friend for such unfair nepotism.

Naruto and Sakura's displeasure with Kakashi lateness. I mentioned this in the previous chapter, but Naruto and Sakura both were vocal about voicing their displeasure with Kakashi for his inexcusable tardiness.

Changing teachers. It's no coincidence that the Team 7 genin were the only ones of the Konoha 12 to each individually choose to switch teachers, nor it is coincidental that they all decided to do so. Young and inexperienced though they were, each of the Team 7 genin could see how ineffective and impotent of a teacher and leader Kakashi was. It only took a little over a year for all three of them to reach that conclusion. If Team 7 ever wanted to achieve their lofty ambitions, the first step in doing so was admitting that Kakashi was an incompetent teacher who would never help them achieve their goals. Thus why all of Kakashi's genin students ditched Kakashi in search of better, higher-quality tutelage elsewhere.

Sasuke's desertion was caused by him realizing that he was never going to find an adequate teacher in his sensei, thus why Sasuke felt compelled to abandon his own disinterested teacher and switch to a new teacher who would actually teach him things.

Right after Sasuke came to the conclusion that Kakashi's tutelage was an ineffective dead end, Naruto and Sakura came to the exact same conclusion. After Sasuke traded out Kakashi for Orochimaru, Naruto traded out Kakashi for Jiraiya, and Sakura traded out Kakashi for Tsunade. Sasuke took the lead on that one, but once he bailed ship, the others did too, all three of them ditching Kakashi.

Considering how bad of a teacher Kakashi was, it's no surprise that all three genin come to the realization that Kakashi wasn't invested in this team, so if they truly wanted to progress in their careers, they couldn't depend on Kakashi anymore, which is why they all turned to the sannin for help when Kakashi failed them as a sensei.

Vacation ranks higher than Kakashi's health, apparently. When Sakura inquires if Kakashi is okay at the end of Guardians of the Crescent Moon Kingdom, Kakashi replies that it's "nothing that a couple weeks of intensive care won't cure". Instead of expressing sympathy for Kakashi's long days of recovery ahead, or at least helping her sensei move out of the puddle of water he is ignominiously lying in, Sakura reacts with delighted glee, cheering and celebrating, because Kakashi's recovery time from his battle injuries equals her vacation time.

I think this shows Sasuke isn't the only one who disrespects Kakashi - Sakura has lost all respect for Kakashi too, which probably started around the time of Sasuke's desertion, which was also when she chose to ditch Kakashi for Tsunade.

Sakura would not be glibly lacking in concern were it Naruto or Sasuke who were seriously injured; she would be upset by either of her genin teammates being hurt. But Kakashi? Apparently she doesn't care about Kakashi. Sakura has lost all respect for her sensei, as moments like this show.

It's especially savage since Sakura is the medical ninja, so caring for people is her job. But she has so little relationship with Kakashi and perhaps she's bitter towards her sensei for Kakashi's bad leadership skills, so that even when Kakashi is seriously injured she is only excited at the fun vacation times for her and Naruto and Lee, not at all concerned or sympathetic with Kakashi's plight.

Apparently so long as Kakashi's poor health benefits her, she doesn't much care that Kakashi is in an injured state requiring intensive care for a few weeks.

Naruto was envious of Guy and Lee's relationship. Between Kakashi and Jiraiya, Naruto got the short end of the stick in teachers, landing some of the worst teachers in the entire franchise. So it's no surprise that Naruto was envious of a very healthy student/teacher relationship that he witnessed, as Guy's love and care for Rock Lee was abundantly clear and so different from the detached, uncaring teachers that Naruto had become accustomed to.

Naruto was charmed by Guy and Lee's hug, noting that it's sweet, and there's an underlying tinge of wistful jealousy in Naruto's words. Not any ill-willed jealousy of course; it's just that Naruto wishes he could enjoy such a healthy and wholesome bond the way that Guy and Lee do.

What really makes Naruto's jealousy clear is when Naruto witnesses Guy and Lee's wholesome relationship in Naruto episode 196, he nods in pleased satisfaction and remarks, "Now that's a student/teacher relationship."

Then only moments after that, Naruto follows up with: "That's a good student/teacher relationship all right. Why can't I have a teacher like that?"

Naruto isn't pleased with either Jiraiya nor Kakashi. Kakashi has failed as a sensei, and even Naruto views his relationship to Kakashi with dissatisfied displeasure, wishing he could have a sensei who actually cared about him instead of the uncaring teacher he got stuck with.

Naruto and Sakura weren't impressed by news of Kakashi's new jutsu. When Naruto returns to the Leaf village after a 2-year journey away, neither Naruto nor Sakura are especially excited by their sensei's company. When Kakashi mentions he is excited to show off his new jutsu, they both ignore it, not caring a bit about Kakashi's new jutsu.

Even Kakashi is disappointed by his former pupils' disinterest in him as he dejectedly notes that they aren't as excited about him as they used to be when they were gullible children. 

Kakashi's "sexual harassment". At the beginning of Shippuden, when Kakashi and Sakura have not much been around each other in 2 years' time, much less worked together, Kakashi warns Sakura not to casually ingest food pills, warning her that they're only for emergencies (as if rushing to save Gaara as soon as possible isn't an emergency, but okay, Kakashi).

Sakura is hostile to Kakashi's advice, which admittedly was pretty condescending in its delivery. Sakura is a medical ninja who undoubtedly knows when one should and shouldn't use food pills. Kakashi was probably trying to be helpful (though he ended up just sounding condescending and rude, as he so often does). Sakura isn't at all pleased with her former sensei, because when Kakashi tries to give her "advice", she angrily crunches down on her food pill in agitation and bounds ahead so that she can talk to Naruto and avoid talking to her former sensei.

Temari, who witnessed the whole brief exchange, inwardly remarks that, "You ever hear of sexual harassment, old man?" Either Kakashi was being genuinely condescending (and he certainly sounded like it) or he was genuinely trying to be helpful, but either way, Kakashi has earned so little respect with his former students that they don't even want to listen or talk to him anymore. Sakura only views Kakashi's "help" with agitation and annoyance. And from Temari's remark, it's pretty obvious that Kakashi is awkward with teens.

Or later on when Kakashi tells Naruto that he's decided that he's finally just starting to like Naruto (meaning Kakashi apparently hadn't liked Naruto before), Naruto gets the wrong idea and assumes Kakashi is making some sort of romantic confession. Kakashi failed so hard at expressing any affection and camaraderie with his teammates when they were young, so now that they are older and have experienced a lot of distance in their relationship to their sensei the past few years, the assumption that Kakashi is a pedophile is more believable than the notion that Kakashi might actually care about his students. That's...wow. I think that says everything you need to know about the state of Kakashi's relationships to his students.

It's not even just Team 7 that views it this way. All of the Konoha 11 also find it more likely that Kakashi would be a creepy pedophile than that he might actually just say something nice about his students or express that he cares about them. Kakashi has so starved his team from a teacher's affection so that when he attempts to express genuine affection to Naruto, Naruto can't even feel happy for the attention. He just feels suspicious, creeped out, and disturbed and runs away in comedic terror, leaving Kakashi chasing after in an attempt to clear up the misunderstanding of his intentions.

This makes it clear that there isn't a particularly strong bond of affection between Kakashi and his former students.

Wanting to trade Kakashi for Yamato. This moment is savagely cold yet amusing, and it's made even more harsh because of the arc it was placed it, juxtaposing Naruto's and Sakura's feelings for their teammate Sasuke versus their feelings for their teammate Kakashi and it's...um...harsh.

As we know, much of Shippuden's second arc's conflict centers on Naruto's hostility to Sai, the "imposter" trying to replace Sasuke's seat on Team 7. A considerable amount of the arc is dedicated to Naruto's stubborn resistance to his teammate Sasuke being replaced by some new guy.

What's hilarious is how welcomed Yamato is in comparison to the hostility Sai faces.

Pretty much on the first day of Team Kakashi's journey to find Sasuke, there's one scene where Naruto and Sakura enthuse that if Yamato buys them a meal for every mission, then they'll happily accept him as captain of Team 7 forever. To make it even more ironic, it is actually Naruto's suggestion, coming from the same guy who is so triggered by Sai daring to replace Sasuke, the criminal teammate who hasn't set foot in the village for 3 years.