Varying solutions have been employed to deal with the problem: 1) keep the historical spelling and accept the pronunciation drift (English, Icelandic, French etc), 2) purge the obsolete spelling to keep it up to date with the current pronunciation, 3) a varying balance of 1 and 2.
Logographic writing systems are the only ones that are immune to the spelling-pronunciation problem as they decouple one from another and continue to convey the semantic meaning of words the logographic system encodes (Chinese, Ancient Egyptian – with caveats). It preserves the historical knowledge at the expense of the future phonetic quality being unrelated to the historical one. This is why we can never be sure how exactly Ancient Egyptian and Chinese languages sounded.
IPA is also a little trickier to adjust to because it has letters not found in English. Someone who's never seen IPA before would have a hard time guessing how to read dʒ or tʃ. (Granted, the point of IPA is scholarly accuracy and not ease of learning so this is an understandable choice the creators made.)
Another thing to consider is that adding new letters creates a lot of overhead for new learners even if it reduces the total # of characters in the alphabet. Ideally someone who has never seen VJScript can scan over a sentence written in it and guess/understand most of it.