I don't consider Kobo as a device that locks me into the Kobo Bookstore. (Amazon does have a better book store than Kobo.) However, I look at it from the perspective of epub vs. mobi or AZW. I buy from BooksOnBoard, Google, Sony Reader Store, Kobo, Barnes And Noble, Diesel & others and read all of them on my Kobo.
I think you should look at it as the world of epub vs. Amazon and in my opinion there really is not a lot of difference to chose from. Epub has more variety, you will get cupon/discount offers for non-agency books. Amazon will have more give-aways and some independent authors you won't find in other bookstores, but, all in all, I find the variety, competitiveness etc., pretty even between epub and mobi.
If you don't have Calibre and the necessary plug-ins to read, whatever you want, on whatever you want, and you can afford it, I would say having an epub reader makes perfect sense. Over the course of a year you would probably get back most of your investment by finding better pricing at other books stores, provided you are a dedicated shopper.
And the same would hold true if you had a Kobo and were looking to buy a Kindle.
Personally if I were to only have one e-reader, I would pick the one that I thought was the best reading experience and not fret about epub vs mobi/AZW. As far as software, despite the speed bumps along the way my preference remains Kobo due to the font selection, ability to fine tune fonts, shelves etc.
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