The protagonist's Stand, Soft & Wet, has lines down the middle of his eyes...
The name itself having '&' in it also hints at the true origin of its abilities, and indeed Josuke himself.
The vertical lines somewhat resemble cat eyes; towards the end, it's revealed that the fusion that created Josuke left Soft & Wet with a version of Yoshikage Kira's explosive bubbles.
Jo2uke uses bubbles, much like his AU counterpart's father's best friend, Caesar.
Part 4 Josuke has the power to restore things, making them whole again. Jo2uke has the power to take something out of things, making them incomplete. Both versions of Kira have the power to destroy things, reducing them to nothing. Jo2uke's power is a middle ground between Josuke's and Kira's.
JoJolion has a royalty subtheme. Stands owned by the Higashikata family have KING in their name, Morioh itself such as its crest (the M has a crown, the fruits trees) and its history, and Kira almost certainly had Killer QUEEN, so Jo2uke is the union between a KING and a QUEEN.
In addition to this, look at the town's symbol from Chapter 1. It's a crown over an M.
Further supported by Soft & Wet and Paisley Park being Prince songs.
The name of the series also fits, as lions are called the kings of beasts. Also, all of the girl names of the (non-excluded) Higashikata family are themed after card suits: Daiya is Diamond, Hato is Hearts, Tsurugi translates to "Sword" (the Tarot suit equivalent of Spades), and Jobin's wife is Mitsuba — "three leaves", or Clubs. This is effective mirroring or foreshadowing of Kaato's ability, alongside establishing a very off-beat theme for the part's main allies.
There is also some thematic naming between family members:
Jobin and Katto's Stands (Speed King and Space Trucking) are both named after Deep Purple songs; both mother and son are shown to share determined personalities and a willingness to do unscrupulous things for the sake of their family (Katto preformed an equivalent exchange between Jobin and a boy who bullied him and tried to set Jobin on fire, while Jobin allied himself with Rock Humans, burned down his own family's orchard, and started to harm or kill people, including his own father and Yasuho, a family friend, in his quest to heal Tsurugi from the rock disease).
Joshu's Stand is called "Nut King Call", a pun on Nat King Cole, and Tsurugi's Stand is named after a song played by Nat King Cole called "It's Only a Paper Moon"; both uncle and nephew are shown to be perverted towards Yasuho, but only Tsurugi grows out of it and treats Yasuho with a modicum of respect.
Josuke and Joshu's relationship is parallel to Jonathan and Dio's when they were kids: a young man is brought in by a loving, wealthy family and proceeds to usurp the place of the favored son. The twist is the roles are reversed in the case that Josuke's in the place of Dio and Joshu's in the place of Jonathan, but Josuke is a nice, caring person, while Joshu's a scummy, selfish prick (but not evil, like Dio). Thinking of this further, Josuke further "usurps" the other favored son, Jobin, when Jobin allies himself with the Rock Humans, then starts acting as an antagonist to them, Josuke, Yasuho, and Rai, and even to his own family in his own quest, only to end up killed.
In Part 8, the Wall Eyes are able to fuse people and things together. Part 8 can be considered an alternate part 4, and one of the things Crazy Diamond could do with its restoration ability in Part 4 was fuse people and objects together when restoring them.
On that note, Part 8 is a fusion of Part 2 (the appearance of Joseph Joestar in the final chapters and the Rock Humans, who are more plentiful and deadly versions of the Pillar Men), Part 3 (the quest of Yoshikage Kira, who is really an alternate version of Jotaro Kujo, to save his mother from an unnatural disease), and Part 4 (the Higashikata family, a protagonist named "Josuke", and the Morioh setting, which also has a dark secret in the form of the Rock Humans' Equivalent Exchange scam).
Jobin's Stand has the power to store heat in objects, while its name, Speed King, brings a completely different power to mind at first glance. However, if you remember that heat is caused by the rapid movement of atoms or molecules, the meaning becomes quite clear.
Chapter 99 has quite a few implied explanations on why Rock Humans are seemingly sparse and hidden compared to regular human beings: first, Rock Humans have no instinctive desire to form communities or to seek out one another unless it's strictly beneficial, meaning that reproduction is likely a rare event in the first place. Second, their way of reproduction, literally abandoning their less-than-insect size newborns out in the forest, is extremely luck-based and likely has a high fatality rate, as the baby's only method of survival is to parasitize off of specific hive insects like wasps to survive, and they definitely can be eaten by spiders or other such creatures before that can even happen!
The little in-universe research documents that nearly all Rock Humans are Stand users. Considering their hellish lives of being abandoned at birth, forced to fend for themselves without any support system, the inability to form connections among humans or even their own species, being unable to conform to human society, and their general parasitic, sociopathic nature, it's reasonable to say that they have enough mental strength to develop a Stand as a survival mechanism.
The implication that Rai has been chasing the head doctor for many years. Suddenly, his Stand ability makes sense.
Why do Rock Human babies parasitize wasps? Organosilicon compounds affect the immune expressions of many species of insects, making them perfect hosts for Silicon-Based Life.
Why was Tooru listening to Elvis Presley's version of The Wonder of You? Considering his Stand's name and his status as the leader of the Rock Humans... he's the King of Rock (going with the royalty subtheme above).
Tooru named his Stand after a Elvis song and his main enemy is Josuke, who shares the name of the JoJo from Part 4, who is known for his iconic pompadour haircut, a.k.a. Elvis' haircut.
Tooru's power initially doesn't seem to have much in common with the time-based theme of the previous series' Big Bad figures, but on reflection, it does bear some commonality. Tooru's power works similar to the Doom Mechanic from video games, in that once affected by it, unless you follow the rules, you will instantly die from some unseen force striking you down in a way you cannot predict or defend against. Though his power only works if he's being pursued, it still plays into the time theme in that, once the heroes start getting affected by his power, they're effectively on a countdown to their own death, given that Tooru also has his stand manifest constantly keep his target's mind on him, and thus 'pursue' him in some form when they make a move or a decision. The final stage of the 'fight' involving the exact time until the new Rokakaka fruit blooms also plays into the time/countdown theme.
In essence, it bears some similarity to the "Groundhog Day" Loop that Kira himself utilized against the heroes.
Not to mention that Kira's "Bite The Dust" activates when someone tries to discover who "Kosaku Kawajiri" really is... or, in other words, when someone pursues Kira.
To compare him more to past antagonists, Tooru is an immortal being with eternal youth, like DIO, and like DIO, both are troubled with things beyond their control: Tooru is troubled with his youth, as it doesn't allow him to progress in life as no one takes a young looking man like him serious, which is why he had his Stand take the form of an old doctor to act as a puppet for him; DIO is immortal, but fears his own fate, which is why he developed the Heaven Plan to have a trusted follower (Pucci) rescue him from his ultimate fate of dying by Jotaro's hand.
Soft & Wet Go Beyond takes Josuke's bubbles to their extreme conclusion. Soft & Wet can create bubbles that can take something out of their target; Go Beyond takes away the bubble itself, leaving behind a projectile that "doesn't exist in this world" and therefore doesn't obey the normal rules of physics. Additionally, Go Beyond also inherits characteristics from Josuke's components: its bubbles are extremely destructive just like Kira's bombs, but can also selectively phase through certain things without harming them - just like how Josefumi was extremely precise with his own Stand and managed to seamlessly graft a Rokakaka branch on a different plant without harming either of them.
Norisuke's Stand is called "King Nothing". By the end, Norisuke, the patriarch of the family, has suffered a lot: his family's orchard has been destroyed, his oldest son is dead, and his ex-wife, for all her faults, is also dead, having sacrificed her life to defeat Toru. He has literally become "King Nothing". On the upside, he manages to survive Jobin's attack on him (Jobin never wanted to kill him), his grandson's disease has been removed, and his remaining children are okay.
However, the song "King Nothing", which Norisuke's Stand is named after, is about a greedy, power-hungry man who destroys himself through his own ambition. That doesn't really describe Norisuke, the Cool Old Guy initially content that his business wasn't booming, but his son and heir to the company, Jobin, who's desire to raise his family's status and break the curse afflicting everyone ends up hurting everyone; he's the one who started working with the Rock Humans, who betrayed him and started to harm him and his family, destroyed the orchard that provided for his family's wealth, gets himself killed, and ultimately leaves Holly Kira comatose with little hope of getting cured. He technically won by getting his son cured, but his actions left a lot of misery before and after his death.
Fumi-kun's introduction involves having his wallet stolen. Then we learn that he's actually Joseph Joestar's counterpart. Once again, Joseph is introduced by having his wallet stolen.
