The PDF format is bloated, complex, and difficult to edit. When someone asks how to merge two PDFs, it's hard to know what to do without some research, maybe use some software, or script, anyway, you can't easily use it.
So, shall we talk about obsoleting PDF?
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 :)