I don't quite understand what it is that you're missing. When I browse PDF files in GoodReader or neu.Annotate, they don't stupidly show the entire paper page with huge empty margins around the text. (They are not iBooks, after all.) Nope, they cut away the needless white space above and below the text, so I do believe they "preserve the zoom" as you put it.
It's always dangerous to judge an entire platform without first testing the best software that that platform has to offer. iBooks is not
the best iOS software to view PDF or EPUB files, just like Safari isn't the best iOS browser. GoodReader seems commonly recognized as the leader on iOS for handling PDF files, so you should at least give GoodReader a thorough test before criticizing the entire platform.