Reading Jojolion speculation makes my head spin. I kean, it basically boils down to:
-Who the hell is the Doc.
-Is Jobin Bad.
-What the Hell are the Wall Eyes and does it tie into Zombie Jesus.
-What is Dio/Diego's influence on the world considering each part has his touch.
-Do the Rock Humans and the Holy Corpse eventually tie into a single stand power granting plot thread.
-Will the Rock Humans continue to be a plot point, and is there a chance at a rock Human Jojo.
I feel at some point Rock Humans straight up replaced the Wall eyes, araki abandoned em, and J worried the ending won't be satisfying.
I don't think Jobin's "bad," but he is probably JoJolion's main antagonist. Everything points to him. Araki's been drawing parallels between him and Josuke for some time now, some of them rather subtle (e.g. Josuke, as Norisuke once explained, is a "yanki," preferring the comfort of soft, fluffy toys—like teddy bears—to that of cold, mechanical robots, which we've seen Jobin admiring in his room). He's also one of the most fleshed out characters in JoJolion, arguably even more so than Josuke or Yasuho.
But let's take a moment and review. Tsurugi, who is obviously rather important to Jobin's character arc, had a ten-chapter introduction, filling us in on the Higashikata family's history with the rock disease and establishing the stakes for Jobin (i.e. Tsurugi's fate and Norisuke's plan to sacrifice himself to save him). Jobin then had a six-chapter introductory arc of his own focusing on his connection to the Rock Humans, who were obviously being set up as a villain group. The next arc returns to Tsurugi and Yasuho's perspective as they continue their investigation of Jobin, who they confirm is working with the Rock Humans. (That's twenty chapters—twenty months in a row, barring any hiatuses that may have taken place during that period—of setup for Jobin! To put things in perspective, that's, like, nine, maybe ten episodes of anime.)
After that, Jobin and Tsurugi take a backseat while Josuke deals with the rest of the Rock Human smuggling crew (i.e. the A. Phex Brothers and Damo), and then Jobin begins actively conspiring against him behind the scenes (with Dolomite and then Poor Tom), sometimes even getting his own hands dirty (like when he attacked Yasuho).
There are other things to consider, as well: Jobin's had several flashbacks, most of them exploring his relationship with his mother and father, and the effect they—and their differing principles—had on his psychological development; his Stand has additional powers that have yet to be revealed, probably because he isn't even aware of them himself; and finally, his wife Mitsuba—who used to be a complete non-factor—has recently become one of the most important side characters in JoJolion, just in time for her husband's conflict with Josuke to come to a head.
Oh yeah, and he's currently in possession of the thing our protagonist has been searching for the last
two years.
No one else has enough character development to rival the emotional weight Jobin would bring to a final confrontation with Josuke, and I don't believe there's enough time left to establish that with another character, nor would it make sense, thematically (given the subject matter explored in JoJolion).
(It's also a simple but clever inversion of Phantom Blood, in that the adopted child, Josuke, is the JoJo, and the biological child is the one conspiring against the family.)
As for the Wall Eyes, they haven't been forgotten; they're central to the story even now. Remember, the only reason everyone's after this specific Rokakaka branch—or the "new Rokakaka," as they call it—is because it was grown near the Wall Eyes, causing it to develop new powers (if Josefumi's speculation is correct), and the Rock Humans, even if they can reproduce that result themselves, don't want anyone else getting their hands on it. The Wall Eyes themselves are likely the result of the Holy Corpse, which, somehow, is still in Morioh. How did it get left behind, and what happened to it since then? That, I'm afraid, isn't clear.
To address your other questions: I believe "The Legend of Johnny Joestar," including what ultimately happened to the Holy Corpse, is incomplete, and the head doctor, Satoru Akefu, may be the Rock Human who killed him (that is, the boulder that crushed his head). While it is true that at 89 years old, he's closer in age to Joseph, Rock Humans hibernate for long periods of time, slowing down the aging process, so who knows. (He's certainly the only Rock Human old enough to have been there at the time, at least that we know of.) Now Diego, on the other hand, I don't think has anything to do with JoJolion, so I wouldn't get your hopes up there, and there being a Rock Human JoJo seems unlikely, since Rock Humans are biologically incompatible with humans.
Overall, I wouldn't worry. Araki's got this. For the most part. (I still have no idea what to make of Karera.)
