Most or all ebook formats and/or readers can now give you the location of text as it is in the printed form, which is arguably useful for citations. However, citing can be done without page numbers. MLA and APA guidelines are notoriously slow to update, but they'll catch up, if they haven't already. You could just specify by the chapter/paragraph/word count. Sticking to page numbers is like sticking to a desktop metaphor. It is a metaphor, it is limited and broken by design.
Preserved presentation only works if you're publishing on paper, or targeting a specific form factor (and thus device). iPads are homogenous enough that fixed-format magazines are available for it, for instance. You can make reflowable content work where you would traditionally use fixed layout. Reflowable doesn't necessitate linear, either, webpages can reflow so that they look similar to fixed-layout designs at wide enough resolutions, or become linear with narrow text. Those of us that have been around a while know how bad the web was when people thought they could just transfer their traditional media without redesigning... or when they thought that some high school kid with HTML experience and a copy of Photoshop could drive your online corporate image. Pushing paper design straight into eBooks has the same problem, but luckily, most of the big players have figured this out already.
That all said, yes, some works are better on something like an iPad which has good graphics, a large size screen, and touch. Others are better linear. Even books of the same sort can be written in different styles which extenuates this. Math textbooks as they're used in primary education work better on tablets, while masters-level mathematics books that concentrate on theory are better on an eReader. (As to which style is better would be a digression, lets not go there...)