I have a third-generation Kindle 3G (edit: [2]), and I'm happy with it - since I never used a cover I got a few broken "pixels" on the display, but these are not very annoying, they look more like ink smudges. I'll probably get the new Paperwhite next (and definitely with a cover!).

For software I use Calibre, I have never used Amazon's own thing. If I buy from Amazon I use the USB cable and Calibre to transfer it, the WLAN/whispernet is always off. That way battery lasts for about a month and I don't get any "unexpected surprises" from Amazon [1]

I have held the Kobo in store and it's pretty much identical in terms of dimensions/clarity/weight. Not sure about the rest.

[1] Like this one: http://www.nytimes.com/2009/07/18/technology/companies/18ama...

[2] Here's one on ebay: http://www.ebay.com/itm/Amazon-Kindle-3rd-Generation-WI-FI-w...

I recommend you an used Sony PRS-350. Smaller than others and best contrast yet I have seen on any ebook reader to date. But no WIFI, if you want that, go with the kindle.