The amazon ecosystem can be nice in terms of ease of use, book selection, etc. That said, mobi as a format is not brilliant. It's handling of simple things like variable margins is a complete disaster, one I wasn't aware of until just the other day. Other types of more advanced formatting like floating images, svg, etc just aren't possible with mobi format.
Epub doesn't have any of those problems, but having an epub reader may mean that you sometimes need to jump through a few more technical hoops.
For myself I use a sony, but buy most of my content through Amazon. This requires downloading to my iphone (though PC users can use Kindle for pc), then strip the DRM so that I can convert to epub using Calibre. I'm quite happy with that process, but admittedly doing all that may not be worth it for the typical user.
If I was going to buy a reader for myself tomorrow I'd go with one of the new Sony readers in a heartbeat, but when it comes to recommending for most friends and family I'd probably still recommend the Kindle...
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