There is a tug of war taking place here. TeX is nice because the documents are formatted for whatever your reading situation happens to be. PDF is formatted for exactly one situation, the A4 sheet you targeted.
But on the flipside, the TeX document will often be ugly no matter how you are reading it, and the author can't easily apply tweaks for aesthetics or readability--many try, hence the TeX markup horrorshow.
Honestly, most of these issues are just a product of .tex's long and storied history. If some foundation plunked down $1-$10 million, it could definitely produce an open source successor to .tex (with extensive, maintained, and documented libraries like Mathematica) that avoids most of the badness.
But on the flipside, the TeX document will often be ugly no matter how you are reading it, and the author can't easily apply tweaks for aesthetics or readability--many try, hence the TeX markup horrorshow.