I'm usually the first one to jump on the English-spelling-is-atrocious bandwagon, but you're not presenting very convincing arguments here:
* c being pronounced either /k/ or /s/ is a perfectly common process called assibilation [1]. Compare Italian "centro" /ch/ as in change, vs. "casa", /k/, as in can't. The general rule is /s/ before e, i, /k/ otherwise. English is relatively regular here.
* x as /z/ is probably some sort of assimilation process when the /s/ in /ks/ would be +voiced. Another reason to pronounce it that way is that anglophones dislike complex onsets (try pronouncing "Dvorak." It's very difficult for English natives not to insert a Schwa /ə/ between /d/ and /v/.
* q as /kw/ is from Latin and most languages using the Latin alphabet retain it in some form.
Letter combos for single phonemes are common as hell. Compare German 'sch', or 'st', Italian 'sci' etc.
"th" representing both voiced and unvoiced interdental fricatives is what's called an "allophone" [2]. Again, this is super duper common, and, off the top of my head, I can't come up with a language without allophones, and I'd require serious proof for the claim that there exists one.
English spelling is a mess, though. But mostly because it's terribly inconsistent. There are several poems about it, which illustrate the point nicely, for example, the Chaos Poem [2].
* c being pronounced either /k/ or /s/ is a perfectly common process called assibilation [1]. Compare Italian "centro" /ch/ as in change, vs. "casa", /k/, as in can't. The general rule is /s/ before e, i, /k/ otherwise. English is relatively regular here.
* x as /z/ is probably some sort of assimilation process when the /s/ in /ks/ would be +voiced. Another reason to pronounce it that way is that anglophones dislike complex onsets (try pronouncing "Dvorak." It's very difficult for English natives not to insert a Schwa /ə/ between /d/ and /v/.
* q as /kw/ is from Latin and most languages using the Latin alphabet retain it in some form.
Letter combos for single phonemes are common as hell. Compare German 'sch', or 'st', Italian 'sci' etc.
"th" representing both voiced and unvoiced interdental fricatives is what's called an "allophone" [2]. Again, this is super duper common, and, off the top of my head, I can't come up with a language without allophones, and I'd require serious proof for the claim that there exists one.
English spelling is a mess, though. But mostly because it's terribly inconsistent. There are several poems about it, which illustrate the point nicely, for example, the Chaos Poem [2].
[1] https://en.wikipedia.org/wiki/Assibilation
[2] https://en.wikipedia.org/wiki/Allophone
[3] http://ncf.idallen.com/english.html