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Online eBook Site
If you're planning on building an online distribution system for ebook readers. I would recommend not to. You would have to build a website and distribution service that offers something that Amazon/B&N/iBooks etc. does not. Books also have ridiculous copyright distribution problems.
If your country does not currently have access to ebooks (certain countries for legal reasons aren't selling ebooks yet) you may be able to make a country-only distribution system. But for that you would need publisher support, the actual electronic books, a way to safely check credit card locality (legal issue again) and charge to Paypal. All while offering a lower price then elsewhere.
eReader OS
If you're thinking about building an actual operating system/programs for eReaders I'd take a look at the Nook. It runs the Google Android OS so mucking around, editing and changing that would be vastly easier then any other eReader's OS.
eReader Software
If you're thinking about building a piece of sellable software in the vein of Calibre (this is what I think your talking about). Then I would recommend building something that can convert almost all formats to any other one to cover all eReaders. I would make it clean and simple as people like one click buttons to sync books etc. and I would probably have the ability to edit Meta-date for books and upload to a website so you can quickly build a large and correct database of books with correct meta-date.
If you are doing option 3 I would instead recommend you work on designing a conversion tool that can convert PDF documents to say ePub quickly and correctly. No one really has a way to convert PDF probably without it fucking up. If you could build that... Amazon, B&N, Sony, Apple would all want to lease or buy it from you.
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