Shisui is a Shinobi of the Genjutsu Body Flicker system, and Jiraiya happens to not be good at Genjutsu.
Jiraiya's apprenticeship is more like a show of support for Shisui; Shisui's strength will definitely plummet after losing his Mangekyo Sharingan.
Jiraiya taking him as a disciple is also telling others that if they want to take advantage of Shisui, they have to go through him first.
Furthermore, a teacher and disciple don't need to be unified in Ninjutsu; they should have a complementary relationship.
Shisui is already a Genjutsu expert, so he doesn't need Jiraiya's guidance in that area.
Shisui can learn a lot from Jiraiya, such as Jiraiya's Fire Release.
Jiraiya's Fire Release is a combination Ninjutsu, combining oil and fire for high power and long-lasting Fire Release.
Also, there are the Summoned Beasts; Shisui's Crow Clone Technique is used in tandem with Genjutsu and is somewhat niche.
The Summoned Beasts of Mount Myōboku provide immense support to a Shinobi.
For example, in the original work when Naruto was chasing Sasuke, if Naruto had just used a Summoning Jutsu to summon Gamabunta...
With Gamabunta's top-tier stats, he could have easily dealt with Sasuke.
But why didn't Naruto do that?
The answer is the director wouldn't allow it; Kishimoto insisted on having Sasuke defect.
Ryou was jealous when he heard Shisui got the Summoned Beast from Mount Myōboku: "How can this be? I suffered the bitterness of defecting, while you guys get all the benefits."
"No, I'm going out to tell the Shinobi Allied Forces that I'm following the clan's orders to resurrect Uchiha Madara."
Itachi quickly grabbed Ryou's cat paw: "Uncle, don't do that. Don't you want to see the Uchiha Clan get better?"
"No!"
Ryou didn't even consider it for a second.
Itachi was puzzled: "Why?!"
Ryou spoke the honest truth: "You guys have to live miserably to justify my defection; the more miserable you are, the more it reflects that my decision was correct."
"Otherwise, wouldn't I become a clown?"
Itachi was a bit angry: "Uncle, how can you be so selfish?"
Ryou was furious: "Good boy, you dare to lecture your uncle? Do you have no manners left?"
Itachi knelt properly and kowtowed to Ryou: "Uncle, I'm sorry! It's my lack of understanding of the rules."
Ryou nodded; the current Itachi wasn't yet the obsessed Itachi who would be brainwashed by the Will of Fire and unconditionally trust the high-level officials' ways.
Giving him a shock every now and then would let him know that the kindness of the Uchiha Clan is greater than the heavens.
Ryou continued the previous topic: "Danzo is just a stinking rat in the gutter, always talking about Konoha as if all his darkness was for the sake of the Village's future."
"But peeling back that layer of bandages, what's hidden underneath isn't protection, but the Sharingan of the Uchiha Clan."
Itachi was shocked: "Sharingan? Elder Danzo stole the clan's Kekkei Genkai? That's impossible, right?"
Ryou sneered: "Back in the Land of Rain, Danzo was killed once by Madara; he was able to escape thanks to the Sharingan. I suspect that eye belonged to one of Shisui's ancestors."
"Specifically, Senior Kagami's."
"I don't have the Byakugan, so I can't see clearly if the current Danzo has transplanted the Sharingan. But judging by his character..."
"He will definitely transplant the Uchiha Clan's Sharingan to save his life."
Itachi rubbed his head: "But the clan's Sharingan are protected very secretly; where would he get a channel to obtain them?"
Ryou shook his head: "I don't know, maybe he picked them up off the ground."
"Regardless, Danzo is definitely the promoter of the Uchiha Clan's destruction."
"Not only does he covet the powerful Dojutsu of the Uchiha Sharingan, but he also delusively wants to eliminate the Uchiha to forever end the Village's future troubles."
Itachi said: "Where's the evidence? Uncle, without evidence, this is just your baseless slander!"
"Evidence? Where am I supposed to find evidence for you? If I say Danzo is a stinking rat, he's a stinking rat."
Ryou's claw grabbed Itachi's face, and immediately the Genjutsu world began to change under Ryou's lead.
Itachi felt his vision go dark, and suddenly he arrived at Konoha Village at night.
Roar—
Then, a beast's roar echoed through the heavens, and a giant demon fox with nine tails frantically destroyed Konoha Village, taking a dozen lives with a single swipe of its claw.
Itachi looked at the demon fox in fear: "What is this?"
Ryou appeared beside Itachi and explained: "This is what will happen in the future. Madara attacked Konoha, releasing the Nine-Tails inside Kushina's belly. The Nine-Tails went on a killing spree under the control of the Sharingan."
The scene shifted; the Uchiha Clan wanted to go and support, but they were ordered by the Anbu to protect non-combatants and were not allowed to deal with the Nine-Tails.
Itachi looked at the Uchiha Clan confined to the clan grounds, full of confusion: "Why? Isn't the clan's Sharingan the most effective power against Tailed Beasts? Why didn't the Anbu allow us to go support?"
Ryou said: "Because that was the Root disguised as Anbu. The Root is Danzo's private force. The Nine-Tails had a summoning contract with Madara, and Madara could summon the Nine-Tails as a Summoned Beast."
"Danzo suspected that the release of the Nine-Tails was inextricably linked to the Uchiha."
Danzo actually guessed correctly; both Madara and Obito were from the Uchiha Clan.
They couldn't completely sever ties with the Uchiha.
The Uchiha were screwed over by Obito for no reason; Obito is the real culprit behind the Uchiha's destruction.
The scene shifted again. After the Nine-Tails attacked Konoha, the Fourth Hokage and his wife died, and Konoha began its decline from its peak.
In a new round of high-level meetings, the higher-ups relocated the Uchiha to a more peripheral position, on the grounds that it was closer to the training grounds and the Uchiha Clan could train better.
In reality, the higher-ups suspected the Uchiha Clan had major involvement in the Nine-Tails incident.
After the Nine-Tails attack, Konoha's strength was greatly diminished. The Uchiha finally couldn't stand the Village's increasing marginalization and sought a Coup d'état.
The scene shifted again.
Itachi put on a mask and became the first Uchiha Shinobi to join the Anbu. The clan had Itachi infiltrate the Anbu to obtain intelligence from the higher-ups.
While Itachi was named Uchiha on the surface, he had secretly changed his surname to Senju; he became a Double agent.
No, Senju Itachi disguised as an Uchiha spy.
The intelligence Itachi gave to the Uchiha was all fabricated by himself, while every conversation at the Uchiha Clan meetings was reported in detail to the higher-ups by Itachi.
Itachi watched in silence. It was a lot of information, but Itachi knew he was very likely to betray the clan and side with the higher-ups.
Because his views were no longer restricted to a single family or clan, thinking with the mindset of a Hokage meant dealing with those who affected unity with cold-blooded means.
And the Uchiha were the ones affecting unity.
The scene changed again. The conflict between the Uchiha and Konoha became more intense, with the possibility of erupting at any moment.
To prevent the Uchiha rebellion, Shisui informed the higher-ups about his Kotoamatsukami, saying he would use Kotoamatsukami to modify Fugaku's will.
Upon learning of the powerful might of Shisui's Kotoamatsukami, Danzo felt apprehension and greed, leading the Root to ambush Shisui.
One of Shisui's eyes was stolen, and he was infected with the Insect poison of the Aburame Clan.
Knowing he had no chance of survival, he entrusted his eye to Itachi and then committed suicide by jumping into a river.
Itachi witnessed his best friend's death and awakened the Uchiha Clan's ultimate Dojutsu, the Mangekyo Sharingan.
Itachi watched this, holding his head in disbelief. If the previous developments were understandable, then this hit Itachi's core values.
"Why? Why did Elder Danzo steal Shisui's eye? If Shisui had used his Dojutsu to change Father's will, couldn't the coup have been prevented?"
Ryou continued to break down Itachi's fragile soul and destroy his core values: 'Why else? He both coveted the Uchiha's power and wished for the Uchiha to overreach and launch a coup.'
"Besides, what difference would it make even if you changed your father's will? Fugaku has always been passive; he's just being pushed by a group of people to rebel."
"The rebellion was so indecisive, not straightforward at all."
"His own home was infiltrated like a hornet's nest, and he still hadn't thought of an Action plan for the rebellion."
"Madara was right; the Uchiha Clan has been raised by Konoha like a flock of fat sheep."