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If the Axis Powers had that kind of cybernetic technology, why didn't they use it to win the war? (The easy answer is "because it was impractical to mass-produce", but that doesn't explain the lack of cyborgs in the postwar world.)
It was probably still experimental and extremely risky, and roughly knowing the german mentality at that time (being german myself and having grandparents that lived at that time), it was probably "Only the elite forces are good enough to becomes cyborgs, but we can't use it on them since it's to risky". Stroheim is the only known cyborg because it was his only way to survive. If there are any others, they're guinea pigs kept away somewhere...
In chapter three, Erina and Joseph tell Smokey about the history of their family. They tell him that Erina saved a child from a sinking ship, and that this child and her own son married and had Joseph together. Later on, near the end of the series, Lisa Lisa reveals to Joseph that she was the child that Erina saved from the sinking ship. How come Joseph doesn't realize right away that this means Lisa Lisa is his mother?
Joseph is clever, not smart. And lucky. But foremost he isn't smart. Caesar on the other hand...
Gee, maybe he's a little distracted by FIGHTING WAMUU at the time?
Denial - let's remember that Joseph had't been having the most wholesome of thoughts towards Lisa Lisa up to that point.
How do we even know Jojo didn't connect the dots? The only thing to suggest he didn't was Smokey's assumption which, well was an assumption.
So, where did Stroheim get all those Mexican prisoners? Did his men just kick down the doors of some poor little village and drag people into cells with the intent of slaughtering them for Santana chow?
Considering that they seem to be a bunch of people who know each other and are of varying ages (i.e. they weren't going to various places asking for teenage boys, for example), yes, that was the implication.
Speaking of Stroheim, why does he have a sight on his machine gun on his abs, where it would do no good, and would be redundant when he has one as a monocle?
It's possible the gun used on him wasn't custom-made, but rather repurposed from some other application, and the sight simply wasn't removed because it wasn't doing any harm.
How did Cars manage to kill the other members of his race? They are only weak to sunlight and the ripple, but they can just turn to stone to avoid dying from the former and Cars couldn't use the latter until the end of Part 2.
Because of the stone masks. The original Pillar Men were just extremely tough/strong long-lived humanoids who couldn't survive under sunlight. All the body modification and absorption powers are a result of the use of a stone mask (they could only partially unlock a Pillar Man's potential without the Stone of Aja, however).
Pillar Men probably have their own way of killing each other, like humans have special ways of killing humans. These methods aren't really relevant to fighting humans though, so they don't come into play in the story.
Where did Joseph get a dress from in the middle of the desert?
He made it from surrounding plants? He found it on the way? He was carrying around? Who knows.
Considering that he carries around grenades and a Tommy gun with him, a dress isn't out of the question.
Maybe the women working for the Germans were living nearby. Joseph found a dress somewhere in their camp/village/whatever, and "borrowed" it.
What are Kars' arm blades supposed to be made from?
Bone? Trace minerals?
It's mentioned that Kar's blades are made from bones. The only reason they don't break when cutting through substances harder than bone is because of the tiny blades moving across their edges.
How, exactly does Joseph know word-for-word what his opponents are going to say when he trolls them? They're people he doesn't know well, so it's not like he can make assumptions about what they might say in a given situation, and he doesn't even mess up the words they're going to say. He does this before stands are introduced, so it's not some secret power of his stand. Is he just straight up clairvoyant?
One guess is that Joseph riles up his opponent so that they're preoccupied with one particular thought, so he's not predicting them as much as leading them. Figuring out their choice of words seems like Awesomeness by Analysis of whatever banter they provided earlier.
He uses his Stand to read the next manga page.
Hes British. He knows what is going to be said because he read the manga backwards, from left to right.
Didn't Araki say sth like, if the Crusaders went back in time and met young Joseph, they would see Hermit Purple wrapped around him? Kinda like an inate ability that later became part of Hermit Purple (Since Stands are just a manifestation of the soul)
Well, we've hamon used to predict the future before(Tonpetty seeing Zeppelli's future). Maybe Joseph was unconsciously using that ability.
How did a bunch of Nazi's manage to get into Switzerland with a war plane during 1939? I know appeasement was a thing back then, but letting a veritable platoon of soldiers just waltz into your lands seems really unlikely. It would almost make more sense if it took place during the war, since Switzerland did let troops from both sides move through their lands (for an extraordinary fee), but prewar Switzerland would absolutely not let a foreign army in without some kind of explanation, and I doubt they'd believe any ramblings about pillarmen and vampires.
Air bubbles?!? Supposedly Kars' armor is made from air bubbles, which creates a protective barrier against lava. Except, ummmm oxygen burns. Now, what they might mean is silica tetrahedra but this isn't how it was described.
And the volcano explodes because of Hamon... oh, nevermind.