Having now published at Amazon, Barnes & Noble, Apple, and Kobo, I've found that all have their strengths and weaknesses, but the big dog is still the leader of the pack...
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While Seven is still in the uncertain (and often torturously long) process of approval with Apple, the rest of my published fiction is available at the "Big Four" ebook stores. I'm not going to claim that the process of publishing is torture with any of them, but they all have their faults and frustrations (and, to be fair, shining moments of quality).
So let's run through the pros and cons as I see them (in April 2014), shall we?
Amazon Kindle Direct Publishing
Pro: fastest approval (usually within hours), best online preview tools, ePub upload means one less step in the pre-publication process, biggest/best marketplace, email notification when books are live/published, easiest to find help (KDP documentation, kboards, and the web in general)
Con: book description formatting is messy, utilitarian (but functional) back-end, two places to post descriptions (Author Central and KDP) is confusing, lower royalties
Kobo Writing Life
Pro: pretty back-end design with fun status messages, streamlined and quick process to upload and prepare books, fastest approval/availability outside Amazon (within 24 hours)
Con: finding bank was a headache for payment processing, non-existent online previewer (download an epub and look at that in an app), WYSIWYG formatting of book synopsis didn’t work (and apparently hasn’t for some time, despite claims of ignorance from Kobo on Twitter), bookstore probably the least searchable/effective of the four, no email notification that books are live/published
NOOK Press (Barnes & Noble)
Pro: pretty back-end design, not quite as streamlined a process to upload/prep books for sale as Kobo (but close!), slightly slower to publish than Kobo (but up in about 24 hours), store/catalog pages are the most useful/elegant
Con: help documentation vague and (sigh) unhelpful, online previewer present but terrible, no notification that books are live/published, weirdness surrounding whether to accept ePub as uploaded or as modified within online previewer (even when online previewer not used)
iBooks/iTunes Producer (Apple)
Pro: predictably, the catalog pages for books are the most aesthetically pleasing (but app-based is a bummer)
Con: why do I need an app (iTunes Producer) to upload a book? why does it have to save a package to my machine as part of the process? no preview of any sort before uploading, approval time way longer than other stores (over a week), byzantine and overly complex sign-up process to even get started publishing through them is not indie-friendly, no email notification that books are live on the store
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So how would I rank them? Amazon is still the easiest to use, the fastest to publish, the easiest to get paid, and has the biggest reach. It's easily #1 (as I knew going in, which is why I published there first). Correspondingly, Apple is easily dead last (I'd heard the rumors and hoped they weren't true, but they were...in every gory detail).
There's not much between Nook and Kobo, but B&N's greater market reach (at least in the US) and higher quality storefront trump Kobo's indie-friendliness and irreverent "cute" factor. At least in my book, and, as I said, not by much.