> Or you can just consider the "book" as a large 2D surface made by tiling pages that the device is a window on and use a simple sliding transition.
You could. The question is if that's a more pleasing experience than Apple's design of emulating physical pages. I doubt there's been any real studies done trying to figure that sort of thing out (simply designing such a study wouldn't be easy). For now, all we can do is go by personal experiences. I've used both iBooks as well as Android apps that did something along the lines of what you describe, and just in my personal experience I've found Apple's approach to be less intrusive (because it acts as my brain expects something physical to act).
> No 3D required
I don't see how that's a plus. Every device Apple ships includes a GPU that's far more than powerful enough to do the 3D animation (even the original iPhone). The Raspberry Pi's GPU is far more than powerful enough to do the same sort of things. That's not to say using 3D is inherently a positive, but the only devices where I can imagine it being a negative wouldn't be capable of doing a sliding transition either (e-ink displays, due to the horrible refresh rates). If you have 3D capable hardware readily available, I see no reason to shy away from using it where it provides a benefit.
> and more intuitive for people who have never seen a physical book (which hopefully will be the majority at some point).
How many people have never seen a book that own an iPhone/iPod Touch/iPad (or any smart phone/tablet)? I'd be rather shocked if the number of people that owned one and that could read, was a fraction of a fraction of 1% of the population of the entire world. Designing a product for a demographic that doesn't exist, and likely won't for 50-100 years, seems quite weird to me.