Most of those languages have made a spelling reform or two that did exactly the proposed radical changes to spelling of words, including common words, to make spelling mostly match pronounciation.
This includes English! http://en.wikipedia.org/wiki/English-language_spelling_refor... covers several major successful (and unsuccessful) English spelling reform efforts since the 16th century.
The Atlantic article discusses the shenanigans of Belgian printers inserting unnecessary letters into words, changing e.g. "frend" to "friend". Spelling Reform 1 (SR1), a failed effort from the late '60s and '70s, would have addressed that and more.
Noah Webster -- of Merriam-Webster Dictionary fame -- spearheaded early American spelling reform. This is why American English writes "favorite" instead of "favourite", "center" instead of "centre", "catalog" instead of "catalogue", etc.
For example, in Spanish, "Iraq" is spelled "Irak"—but only as of 2010! The change came with justifications: that it avoids the use of "q" outside of the digraph "qu", and that the terminal "k" is nowadays more familiar in words borrowed from other languages.
Japanese is a famously difficult language, but in the past century and a half, they've had multiple reforms which standardized and eliminated characters—there are more changes in the works, but it looks like they'll get new characters, such as "gaiji".
As an English writer I feel left out.
It's pronunciation that's hard to guess from kanji.
頭が痛い (atama ga itai)
頭痛がする (zutsuu ga suru)
harakiri (腹切) is seppuku (切腹) backwards
Several different readings is a bit of an exaggeration, it's more common to just have a kun'yomi and on'yomi reading, and on average I think the number of readings you'd know for a character is between one and two.
Purely from personal experience, I hear adult native English speakers (including myself) mispronounce words all the time! It's a common mistake to pronounce a word as if it were borrowed from e.g. French when it was really borrowed from Greek or Latin. So if you want to know how to pronounce "ch", you might say /ʃ/ if it's French and /tʃ/ if it's English. This seems to me like another variation on the same problem we have with reading Japanese, where characters have Japanese and Chinese readings.
昨日 is sakujitsu or something? nope, it's kinou 明日 is just as bad
行く can be both iku and yuku, good luck telling them apart