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Kindle is held comfortably in either hand, with buttons on both sides. Don't remember about the Sony.
And you can absolutely put your Mobi files on it. I do it all the time. I convert things as needed, but any mobi file you can get (especially free ones from here, feedbooks, etc.) can be put on the Kindle. And here and Feedbooks also has a way to download books directly TO the Kindle from here.
Bookmarks are as many as you like on the Kindle.
I don't know much about Calibre. It doesn't work for me. I'm on a Mac and use Parallels to use MobiPocket creator to turn most things into ebooks. But that doesn't convert other ebook formats - just pdfs, docs, html, etc.
You could also use Stanza. It seems to do an okay job except where tables of contents are involved, and then it royally screws that part up (at least in mobi files.)
Not being able to "flip through a book" is a big problem for me. I tend to use the search a lot because of that.
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