While most of the comments seem to talk about the issue of programmers vs designers, and management cutting corners, only a few of the comments hit upon the inherent nature of varied layouts.
Just as a website needs to take into account different web browsers and different screen layouts/sizes, and user-controlled fonts, so does an ebook.
Designers still hate the fact that a website cannot be controlled by the designer like printed material. How many designers embraced Flash because of the absolute control it took away from the user? The designers tend to view things as stationary, and that is the opposite of all the options available on the web, and in ebooks.
Certainly, we need designers to assist in any creative project. And designers should probably consult a little more with programmers to see if their ideas can be implemented in a more efficient way. Steve Jobs is a perfect example of creating a team of visionaries, designers and programmers.
The problem with an ebook, besides the multiple formats of epub and amazon and others, is the user options. We can read on our phones, on tablets, on computers, in apps on the computers, in browsers. And many reader applications allow for some personalization, like changing colors, fonts, font sizes. So, like a website, we are stuck with basic text formatting to allow for free-flow of paragraphs and dynamic pages.
PDF is NOT an ebook. It is a digital format of a printed page, designed as if to be printed. It certainly looks great, and if put into a flash application, can look like a real magazine with page turning, etc. But, will that work on a 3.5" screen? How will it handle zooming in and out?
I think we need to look at the overall purpose of the product. If it is a magazine, with images and multi-column layout, then certainly the "e publication" needs to be locked into it's print perspective like a PDF. But, if it is a novel, or any book where the message is in the words, then proper formatting is needed for free-flowing text in various sizes. I am not going to view Time Magazine on my phone, but I might want to read an article from Time Magazine. So, now I need two formats.... text only, and Image Layout.
Let's just learn the proper techniques for the layout output we are looking for, and use programmers where needed, and designers where needed. And get those MS Word office workers out of the process unless they learn about formatting with styles, page breaks, tabs, etc. Not many people can know everything, and do everything. Just because the person down the hall makes cool signs for the wall does not make them someone that can create a proper ebook.