G, J, K, U, W, Y, and Z are all characters that aren't used in Latin (in the case of G, J, U, and W, because they didn't exist; in the case of Y, it is used in Greek words but doesn't represent a sound that's possible in Latin; I'm not sure if Z was used in Greek words or not. K is just a Greek letter -- since it represents the sound written with C in Latin, it is never used at all).
Latin wikipedia isn't exactly an ancient source. Without bothering to read the article, why do you think it has a subhead of "Fontes_de_vita_C._Iulii_Caesaris_praecipui"?
You think "cum granulo salis" is evidence for G being an original part of the Latin alphabet, while not being evidence that U was an original part of the Latin alphabet?
G dates to the classical period. But, as I pointed out above, it's still intrusive enough then that Caesar's praenomen, Gaius, is written C, not G. The name is older than the letter, but younger than Latin writing.
What do you mean by "special"? If you mean "can be encoded in US-ASCII", then that's a bit circular, because that character set was obviously designed to encode the English language. In a parallel universe where the ancient Romans had designed a character set, it would be the English language that would require all those weird unicode characters like "J" and "U" (which didn't exist in the Roman alphabet).
It actually seems fairly intuitive to view Ä as a cheap knockoff of A whereas U and W are independent forms.
That would be wrong -- as the name suggests, W derives from U, similarly to how G, J, R, and U derive from C, I, P, and V. But it shouldn't be hard to see the intuition behind the idea that s is a "natural" letter and š is an unnatural modification.
It's almost like a lot of languages have a shared ancestry.
Differences may be unusual to you. Are ș, î, or ț unusual because they don't exist in English? Those phonemes aren't common in English which is why we don't have distinctions for them, but they're important in Romanian. Not unusual at all if you're Romanian.
By your logic, 대한민국 characters are weird and unusual also, and so on...
Yes, hangul is unusual, because there's only one language that uses it. Duh. Latin characters are less unusual because tons of languages use them. I'm not sure why this is difficult to grasp.
When I think "weird special English letter" I think Œ, as in fœtus. Granted, in American English it has been eliminated almost completely and even in British English it's now often seen as a bit archæic (pardon the pun) but it's still there and to me signifies "English" just as ß signifies "German", ø signifies "Nordic", ı signifies "Turkish" and é signifies "French".