This is for an extremely first world problem, but let me make my case:
I own a Kindle Oasis and I enjoy reading manga on it because of the high pixel density and the experience of reading on e-ink vs. reading on LCD/OLED. So naturally, I enjoy reading doujins on it as well.
However, the problem with many manga releases on the Kindle Store is that they don't have a proper Table of Contents, so jumping around chapters is impractical. Because of this I'll usually procure my reading as image files elsewhere and manually convert them to .mobi myself after sorting them into folders by chapter. The program I use is called Kindle Comic Converter, or KCC, and that program will automatically generate a Table of Contents based on the folder structure of the .zip file you feed it. So my workflow for this is to organize my manga into chapters, put each chapter in it's own folder, then feed the whole .zip to the conversion program to read on my Kindle. The only gotcha to this process is that KCC will order the chapters alphabetically, so the folder name has to start with "Chapter XXX" or similar.
Most .pdf files for books I've downloaded from this site already have bookmarks for each chapter and this gets me 90% of the way there, but there are two big problems with this for me. First, .pdf files can't be viewed in full-screen on a Kindle: there's always a small margin around the edges of the screen to show you which page you're on. Comics converted in KCC can be viewed in full-screen, as can manga or comics purchased through the kindle store, so simply copying the .pdf to my Kindle isn't ideal. Second, converting from .pdf to .mobi doesn't extract the bookmarks from the .pdf and takes a long time besides, at least the way I'm doing it through Calibre. Amazon offers their own Send To Kindle service that might work automagically for me, but the filesize limit is 50MB which nearly everything on this site runs over.
Thus I'd appreciate it if book releases weren't just an archive of .pngs, but also had a folder structure to separate the book into chapters and keep said chapters in order when viewed alphabetically. This is a decently sized change that only benefits a few people, but would make it an order of magnitude easier to prepare these books for reading on e-ink devices.