Wow. I have an H2O. It has only trouble for very big files; but I usually only use EPUBs and some text PDFs.
My main grudge is they removed support for CBRs months after I purchased it, and that's one of the main reasons for choosing a Kobo for me.
The next one is I can't resize images in EPUBs, so any kind of map or graphic gets stuck at full width.
What ebook format are you using?
Everytime I test an epub file with a variety of ebook readers (devices or apps, it is the same), they are never formatted the same way, unless it has barely any format at all.
And diagrams are always a pain, because they usually get painted too small, and readers usually haven't got any zooming feature for images.
And I am only reading them; I can't imagine how bad it can be for authors.
I suspect ebooks are in the same state as HTML 20 years ago: a total PITA to get straight in all browsers. Besides, ereaders allow users to customize ebook design much more than browsers, and we users take advantage of it much, much more than we do as browser users. Being able to customize font family, size, line height, etc. is one of the main selling points of those devices. Kobos even allow you to use your own custom fonts in any book.
You could use PDF if you really need coherence, but, really, I hate PDFs on my ereader so much I may have read two or three in 10 years.
My advice is: forget about getting the same design everywhere, aim for getting a good one anywhere, pay attention to diagram size and resolution. Otherwise, you may end like a Lovecraft character at the end of the book.
@jgg this is an epub of a book I wrote and produced using pandoc. I bought the kobo for QA purposes and it looks like I got some work to do.