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I have both the Kobo Aura HD and the Kindle Paperwhite 2 and they are both great ereaders. The lighted screen on both is wonderful if you want to read in bed or in a low light situation. Both allow you to put your books in collections although you can't put books in collections through Calibre with the PW as you can with the Aura HD so if you would be sideloading your books the Aura HD might be a better fit for you. I also really like the larger screen on the Aura HD. The Aura HD also has a micro SD card slot so if you want to hold your whole library on the reader you can. The Kindle has no card slot.
Depending on where you live it may be easier to get a Kindle than a Kobo. I've also had much better experience with Amazon as far as customer service when having problems with an older version Kindle. Recently my Aura HD broke and Kobo makes you jump through hoops to get a replacement. Also, Amazon has tons of free Kindle books you can get.
The wifi only Kindle PW 2 is less expensive than the Kobo but the new Aura is less than the Aura HD although still more than the Kindle. The new Aura also works with more formats than the Aura HD but has a 6 inch screen like the Kindle. I also have a Kobo Glo and it's a nice little reader with a 6 inch screen.
Like everyone else has said, it's a personal decision but you would likely be happy with either choice. I would recommend googling Apprentice Alf and making friends with the tools so you can back up your books and really own them no matter what happens to the ecosystem you choose. Calibre will allow you to organize and change formats for your library so you can use the books no matter which new readers you may choose in the future.
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