I would imagine that a plain text file would be a nightmare to read, with no formating or chapters/bookmarks etc. At least with PDF Expert you can double tap to zoom, embedded chapters and links work, you can add bookmarks and the app remembers where you closed so you can pick up where you left off. Downside is page turning would be a scroll up/down, but you can jump to any page. Also, you can't change the font etc but as the original formatting is retained, this shouldn't be a problem.
One big negative for me is that their support sucks. I've emailed them twice about a point and have heard squat from them. I've two simple PDFs that won't display. But, Ive more complicated PDFs that other viewers trip over that PDF Expert handles with ease.
I can't imagine having to zoom in/out while trying to read an ebook. Also, changing font size is a nice luxury. Sometimes, you just need bigger text to comfortably read. And I may be an outlier, but scrolling up/down to advnace pages in any format makes an ebook harder to read. Tapping to advance a page is much more natural and user-friendly.
Reading a txt file is not as bad as one would think - and I've tried both formats. A txt file is like puddy - you can modify it to however you want to fit your needs - it's not stuck in any one form. As for it having no formating for chapters, yes, that is one negative. However, I never see this as a problem because Stanza always bookmarks where you left off last. If you read a novel from front to back, I don't really see the need for jumping to different chapters. For a technical book or textbook, this would indeed be a big issue. As for other bookmarks, you can place a bookmark anywhere you want in a txt file using Stanza.
Therefore, for me, txt files are best for novels/literature and PDFs are best for technical books, scientific articles, textbooks.