Why do some languages have a writing system that closely represents the way the language is actually spoken while other languages have a less clear writing system?

No writing system in the world can represent the way a language is actually spoken; the two are entirely different systems of signs - writing is a system of visual signs while speaking is a system of audio signs. We humans think that our visual signs represent our audio signs; they don't. But yes, they do provide us a system to work with and carry out our daily business. The mismatch between speech and orthography seems to be a product of historical development of a language. In the historical process, certain languages have evolved in contact with other languages, and they have gone through heavy exchange, give and take, thus making it difficult to keep a rigid system of speech and writing, undergoing regular change in both. Languages like English fall in this category. Other, less historically disturbed languages or languages guarded by certain rigid norms remained "purer" maintaining what was originally devised as a closer match between speech and orthography. Classical languages, like, Sanskrit, Latin and Arabic fall into this category.

This is just an approach to answer your query, and frankly speaking, to pinpoint exactly "why" certain languages display more of a mismatch between speech and writing compared to others is next to impossible. But sure, classical languages do show less mismatch. Why? Difficult to say.