[ufo]

I think the spelling difficulties have more to do with English not having phonetic spelling than with it having many loanwords, prefixes or suffixes. I speak Portuguese and we have lots of loanwords as well but after a while they are all spelled like the rest of the words are instead of copying the original spelling. And every once in a while there is a spelling reform to replace archaic spellings with more modern forms (this never happened with English because it was politically unpopular)

[maffydub]

I think the cause of a lot of the bizarre spelling in English is the "Great Vowel Shift" - basically, sometime between 1350 and 1700, most uses of most long vowels changed their pronunciation.

Obviously (because this is English), the change didn't apply universally, but it applied widely enough to move our pronunciation out of sync with the European languages it was derived from.

See https://en.wikipedia.org/wiki/Great_Vowel_Shift for more detail.

[pbhjpbhj]

How words are spelt (!) in en-gb definitely owes a debt to the word origin, or sometimes the imagined origin ...

http://mentalfloss.com/article/59320/5-words-are-spelled-wei... has a couple of nice examples.