[gettalong]

There is no reason to abandon PDF. As was already stated the main purpose of a PDF is viewing something as the author has intended, it should not be dynamic like a website. And editing is possible but not the intended use-case (and therefore harder to get right).

As for merging PDFs you first need to know what the user wants. Just merging the pages? Or should AcroForm forms be merged? Should the outline be merged, too? Depending on the answers you can then proceed with the merge. Simply page merging can be done with any tool, merging AcroForm forms or outlines may require more advanced tools.

PDF is actively worked on at multiple fronts, for example, support for HDR, newer image formats, maybe variable width font embedding, better re-flowing capabilities when this is needed (e.g. for small-screen devices)...

And with the ISO PDF 2.0 specification now freely available, anyone can join in :)