Transliteration, Scripts and Orthography

Something of a scattered rant here.

Transliteration and Orthography

Transliteration is the process of writing a word not normally written with the Roman alphabet into Roman alphabet letters for people who don't understand a language's main script. There are consistent systems of doing so from one particular language, but this can lead to weird orthography.

Why are transliteration systems for various languages into the Roman alphabet so often at odds with intuitive pronunciation? 

Some examples:

* Why does transliteration of Maori transliterate an "f"-like sound as "wh"?

* Why does transliteration of Vietnamese transliterate a "wh"-like sound as "ng"?

* The revised Romanization of Korean adopted in 2000 by the South Korean ministry of culture is much further from a natural pronunciation of the transliterated words the way that they sound in Korean than the previous McCune–Reischauer system (which admittedly had too many accent type marks for the Internet and wasn't perfect itself). The new system is unambiguous leading instead to consistent error by the uninitiated instead of allowing people to sometimes get it right, especially if they've heard the word before but not seen it written.

* Why does the letter "X" used in so many disparate ways in transliterations, having different sounds, for example, in words derived from Greek, Chinese and Aztec?

It would be nice to have a simple reference of how non-intuitive transliterations work in all of the world's major languages in one place.

It would also be nice to have a list of what phonemes are absent in American English that are present in other major languages, and what phonemes are present in American English that are absent in particular other major languages.

Scripts

Why does Japanese of all language have three phonetic scripts (two based upon syllables that basically code every possible syllable in two different ways, and a Romanization)?

Japanese has a fairly small set of phonemes, pronounced in a consistent way, with few complexities such as a vowel later in a word influencing how a vowel earlier in the word is pronounced, few silent vowels and consonants, few vowels that are implied but not written, very few consonant clusters, little use of tone other than a pitch-accent system, etc. It could totally manage with a short and simple alphabet along the line of Hangul in Korean whose phonology is similarly straight forward.