Well, in my experience with a Kobo, and ibooks on my iPad, they both handle relatively well with novels, or other books that you want to read from beginning to end in a straight line. However, most publishers make electronic copies by taking a printed manuscript, and just running it through a large scanning machine. It does text well, but does pictures poorly, as well as charts, and any book that is an "irregular size," shall we say. If you're getting a book that's 15x15 glossy photos, and have it reduced to fit on the iPad, even if they fit on the screen that's going to be a sucky way to look at them, imo...
Also, because of the way that they work by clicking or flicking from one page to the next, they're not good for instructional or academic books either. I.e., anything where you want to flip back and forth between a middle page and the footnotes or endnotes.
It varies from book to book, publisher to publisher. More books are being properly formatted as e-book popularity rises. If you buy from a good e-bookstore like Amazon's and it turns out the formatting makes the book unusable, they will not only refund your money, but also often stop its sales till the publisher fixes it. So you risk nothing by buying from Amazon and seeing whether a book is usable.