Today there are typically two ways of publishing and reading ebooks on mobile devices. You either use a reader app, often from a device maker (e.g., Kindle, iBooks) or you use a dedicated app written on that platform for that particular work (e.g., The Elements or Solar System for iPad). Some of those dedicated book apps are terrific but I think they're a symptom of one of the more significant problems in the world of ebook evolution.
I love it that there's so much experimentation going on now with apps, but oftentimes they're one-off's that require a reinvention of the wheel for each new product. I also hate the fact that we're creating a bunch of book apps that don't talk to each another. One of the simple features I've been asking for in reader apps is the ability to search across a library. It's far more likely we'll see that implemented in the Kindle reader, for example, before we'll ever see all these individual apps communicating with each other.
What really needs to happen, IMHO, is for the reader apps to evolve much faster than they are today. Apple just added the ability to separate your ebooks into different shelves in the iBooks app. What a concept. The Kindle app has been around much longer than iBooks and it still doesn't support something as simple as this.
Awhile back I suggested that Amazon ought to get out of the hardware business and focus all their efforts on making their reader app the finest on the planet. Even though they're not taking that advice, I've got a new idea for them to consider: Turn the Kindle apps into open source projects and enlist the help of the community to enhance and improve them. Imagine how many great new features would be implemented in this model. Rather than being limited by the fixed (and apparently small) number of developers assigned to the internal Kindle apps dev team they'd suddently have access to as many developers as they could recruit to the open source project. They could create a world class set of apps and quickly distance themselves from the competition.