Have you used a Kindle? It's not small nitpicking, sometimes they layouts it makes are laughably bad and hard to read. Basic stuff that anyone who has read a book would notice at some point and it hasn't been fixed in YEARS.
As for full justification, I don't really mind it. It's not a pain point for me. If I wanted to be picky, I could come up with a list of minor issues.
The problem is the Kindle is the best reader out of a category of really shitty products.
I've started seriously contemplating going entirely to scanned, pirated PDFs and simply mailing the author a check the retail cost of the book. I'd love for technical books to start rendering PDFs for multiple common ereader screen sizes. Journal articles are too much to hope for.
Google Play Books supports having both EPUB and PDF for the same document, and, I believe, chooses between them based on screen size or other platform features. I don't think it supports having prerendered pages for different layouts yet, but certainly the "buy a title, which might have multiple formats for different devices" thing is already established there, so its not a big jump to see it being done with more specificity.