Seemingly there exists a discrepancy between the manga and anime portrayal of the relationship between Sasuke and Shisui.

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In the manga, it seems inferred that Shisui and Sasuke were not especially close. Going off the manga alone, one might wonder if Sasuke even knew Shisui at all. We only get a few mentions of Shisui when Sasuke is around. The first is when Sasuke hears the news about Shisui’s death, though almost bizarrely, Sasuke doesn’t seem overly concerned or bothered by the news of the murder that his brother allegedly committed, perhaps reflecting a young child’s confusion of a situation he isn’t much informed about. Sasuke is more shaken by Itachi’s violent, aggressive behavior than by the news of Shisui’s suicide, which seems to imply an uninvolved relationship to the famous Shisui Uchiha on young Sasuke’s part. Of course, Sasuke was significantly more horrified the night of the massacre when he realized that Itachi actually did kill Shisui, so perhaps Sasuke’s lack of initial concern is entirely down to Sasuke being absolutely certain that his older brother would have never murdered Shisui.

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The anime, however, paints a far warmer and more fleshed-out depiction of the bond between Shisui and Sasuke, showing Shisui as something like a second older brother figure to young Sasuke.

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Personally, I think the anime's expansion into Sasuke's relationship with Shisui is more plausible and fits in better with fledging out Sasuke’s pre-massacre life, so prefer the anime’s take on Sasuke’s relationship to Shisui. One could argue that the anime depiction of the relationship between Sasuke and Shisui strays from the original manga, seeing as how Sasuke appeared more indifferent and neutral on the tragic news of Shisui’s premature death (though that could just be due to shock). But since Shisui is Itachi's best friend (and seemingly Itachi's only friend aside from Izumi, his ex-teammate Shinko, and little Sasuke), it seems more probable and realistic that Sasuke would know Shisui, and know him well, as the anime depicts. Otherwise, Sasuke not knowing or caring about his older brother’s best friend is strange considering how much Sasuke adored and loved Itachi. Itachi having only secret and nameless friends that Sasuke wouldn’t know seems unnatural. Itachi tends to hide things from his family, but even so, hiding Shisui from his family seems over-the-top unnecessary, even for Itachi, erratic and nonsensical as Itachi’s behavior usually is.  

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The anime shows that Shisui behaved with brotherly warmth towards the young Sasuke. Shisui was good with kids - so good, in fact, that judging from the cliffside scene in The Two Uchiha, Shisui is far more suited to the role of big brother than Itachi ever was.

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When Sasuke discovered Itachi and Shisui meeting at their special spot to secretively discuss tense political affairs, Sasuke demands that the two older boys tell him what they were talking about. Itachi bluntly tells Sasuke’s he’s too young to be privy to such secretive discussions.

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In response, Sasuke complains that, “What? I’m not a part of the group now?”

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Sasuke wants to perceive Itachi and Shisui not as part of a duo, but as part of a trio with him as the proud third component of that triumvirate. This scene again highlights Sasuke’s interconnectivity with his clan, as well as Sasuke’s desire to belong. Sasuke strives to be included and accepted, and he detests being pushed aside. Itachi is affectionately amused by Sasuke’s enthusiasm, yet knows that Sasuke isn’t yet ready to be a part of the duo that he and Shisui make, since Sasuke is far too young to be ready for political strife and heavy responsibility. Though Itachi is being honest with Sasuke, he thoughtlessly brushes Sasuke aside, sending the message that Sasuke is too young, too irrelevant to what the big kids are doing.

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While Itachi pushes Sasuke out of the group that he and Shisui form, Shisui steps in and pulls Sasuke back in. Of course Shisui isn’t stupid enough to spill the beans about the political strife between Konoha and the Uchiha clan to a 7-year-old, but Shisui teasingly calls Itachi out for being a “horrible big brother” for always leaving Sasuke out of things. Shisui doesn’t brush Sasuke aside, but rather allows him into the duo’s circle by teasing Sasuke, allowing him to feel like he belongs with the two older boys.

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Shisui proves how much better he is with kids by conspiratorially telling he’ll fill Sasuke in, a remark that initially worries Itachi. Shisui smoothly lies, telling Sasuke that he and Itachi were discussing who of them is the strongest, and Shisui claims he believes himself to be the stronger of the two.

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Perhaps one of the most comical yet tragic aspect of this scene is how it clearly illustrates how ill-suited Itachi is to be anyone’s older brother juxtaposed to how well-suited Shisui is to be a sibling. Ironically, Itachi’s honesty with his brother ends up pushing Sasuke away more than Shisui’s blatant lies do. Though Shisui is excluding Sasuke from the actual discussion he and Itachi had been having, he does so warmly and fondly even while lying, yet that makes Sasuke feel more included within the group than Itachi’s honesty did.

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Shisui managed to make Sasuke included in their group with some good-natured jabbing at Itachi’s skill as a shinobi, a topic Shisui is likely well aware that will get Sasuke energized and riled up. It appears Shisui is well-versed in Sasuke’s unyielding devotion to his older brother, seeing as Shisui intentionally challenges Itachi’s strength, declaring he believes he is stronger than Itachi. That’s all it takes to get Sasuke fired up and passionately defending Itachi’s reputation as the strongest ninja in the Ucihha clan. Shisui is thoroughly amused by Sasuke’s passionate and loyal defense of Itachi, as Shisui appears to find Sasuke’s loyalty to his brother both humorous and precious.

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Shisui treats Sasuke with sincere respect that isn’t condescending, even apologizing to Sasuke for stealing Itachi’s time from his little brother. Shisui expressed warm inclusivity towards Sasuke, recognizing that the kid wanted to be accepted by his elder friends, though his innocence and young age made it difficult for Itachi and Shisui to relate to when they had so much going on in their lives that little Sasuke couldn’t be allowed to know about.

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Sasuke is most receptive to Shisui’s good-natured indulgence, while Itachi is gently rebuked by Shisui as he realizes that Shisui handled things better with his little brother than he had.

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Being one of the only scenes where Shisui and Sasuke interact, one might note from Sasuke’s apparent delight at finding Shisui indicates that Sasuke is quite fond of Shisui. More than that, Itachi and Shisui were probably the “cool kids” in Sasuke’s life, the older kids he admired and so wanted to be a part of their group, which is why encountering Shisui and Itachi speaking secretively together made Sasuke enthusiastic to know what they were saying to each other, demanding for Shisui and Itachi to tell him. Uninvited to their group, Sasuke nonetheless strives to become a part of it, wanting to belong with the two older boys despite being a bit of an outsider because of the age gap between them. Shisui and Itachi are on a different walk of life than Sasuke is, making it a bit tricky for the two parties to connect on some levels.

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In any case, Sasuke and Shisui get along famously between Shisui’s good-natured warmth and Sasuke’s admiring cheerfulness. Their personalities work well with each other, and Sasuke seems to admire and respect Shisui similarly to how he respects and looks up to Itachi, if to a lesser degree, seeing how Sasuke passionately defends his brother’s reputation as a warrior at the expense of naming Shisui as clearly the weaker of the two.

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Sasuke smiles frequently around Shisui and seems entirely comfortable and at ease with him, unafraid of speaking his mind around the older Uchiha boy; Sasuke’s not at all reserved or closed-off with Shisui, but rather transparent and full of enthusiasm.

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A frame in The Two Uchiha showed a memory of Shisui showing Sasuke a shuriken, possibly implying that Shisui took time to train with Sasuke. An interesting aspect of this frame is that Itachi is aloof in the background, watching the frivolities but not participating in them. Whenever Shisui is around Sasuke, Itachi tends to take a backseat, while Shisui is adept and savvy with children, entertaining young Sasuke without being condescending and impatient or too busy for Sasuke, the way Itachi often is when around his younger brother.

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In Shippuden, Tobi’s revelation that Danzo possess Shisui’s eye evokes far more emotion in Sasuke’s anime persona than his manga counterpart. In the manga, Sasuke barely even registers that Danzo stole Shisui’s eye. Yet in the anime, Sasuke is visibly angered by that information, as the shock of the news that Danzo possess Shisui’s eye makes Sasuke recall the memory of the day he learned of Shisui’s death, causing Sasuke’s hatred to increases as he scowls at Danzo, realizing that the man who murdered his people also stole Shisui’s Sharingan for his selfish purposes.

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As for Shisui, he was very fond of Sasuke, treating him like a little brother. In The Two Uchiha, Shisui happily muses how great it is to have a family every time he sees Sasuke and Itachi together. Shisui’s own family life wasn’t in the best of shape, as his dad died when he was young and Shisui had no siblings. Personally. I think Shisui envied Itachi for having a little brother. I imagine that Shisui wished he too had a younger sibling, seeing as how Shisui was an extrovert, friendly and outgoing and people-oriented. One can’t help but imagine Shisui envied the bond Sasuke and Itachi shared. From Shisui’s musings as he watches the two brother interact, it seems Shisui finds it pleasurable just to watch those two and admire the special bond they have from a distance. Shisui might’ve even considered Itachi and Sasuke both as brother figures in his life, Itachi as an equal and Sasuke as that cute little brother he wanted but never had. Shisui even states that part of his motivation for wanting to resolve the Uchiha clan’s conflict with Konoha was specifically to protect the bond that Sasuke and Itachi shared and equivalent bonds. It is also why I personally think Shisui would’ve opposed the Uchiha massacre and would’ve never agreed with the decisions that Itachi made to destroy the clan. I believe Shisui would have wanted to try harder to protect the familial bonds within the clan, which Shisui saw as precious things deserving protection. But that’s just my two cents; fans are free to debate whether they think Shisui would have supported or opposed the massacre. Though I might add that in Itachi’s Story: Midnight, Itachi similarly believed Shisui would’ve opposed the massacre.

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Although Shisui makes friends with Itachi, that doesn’t automatically mean he wanted a package deal with Sasuke thrown in, seeing as how Sasuke was still very young, and older kids don’t always want to be stuck watching over younger kids, who they can view as a nuisance. Yet Shisui never treats Sasuke as a nuisance, but with a good-natured respect and attention, apologizing to Sasuke for taking his brother away from him and including Sasuke in his and Itachi’s group, even when he didn’t have to, as Itachi made clear. Shisui could easily have completely detached himself from Sasuke and ignored the kid. Yet Shisui is accepting of Sasuke, making him feel like he’s included in Itachi and Shisui’s inner circle.  

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Sasuke and Shisui appear to have a smooth and easy-going cheerful dynamic, both respectful of each other and evidently liking each other very much.

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Seeing as how Sasuke, Itachi, and Shisui proved to be not just the strongest of their clan in their era, but some of the strongest shinobi of their entire age, it’s interesting to speculate what kind of name these three would have inked for themselves on the pages of history. They were immensely strong (though as the youngest, Sasuke lagged behind the other two for a while before springing far beyond both of them in terms of power) and they were close friends, so it would be interesting to see what kind of name they made for themselves as a trio had Shisui survived and the Uchiha massacre never taken place. Allowed to live together in harmony, these three would have perhaps become an unstoppable force, a fierce foe to all they opposed. One can’t help but ponder the widespread influence and reputation Sasuke, Itachi, and Shisui might’ve accrued, politically and historically. No doubt they could’ve grown to become a terrifyingly unstoppable foe, a triumvirate that would go down in history for their many feats. Alas, things didn’t work out for the three friends so that story was never to be.