I'd personally go with the Kindle, because I can't stand the way the touch layer on the 600 degrades quality and adds more glare. The Kindle also uses the newer Pearl screen which generally gives better contrast. For me the quality of the actual reading experience is what's most important. Then again if the screen quality on the 600 doesn't bother you...
IMO Mobi vs ePub isn't a big difference for most books and you can always go AZW3/KF8 instead of Mobi if there's an ePub that has some special formatting you must have. Collections definitely are a bit easier on the Sony though.
I assume the Kindle's browser will work with Box in a similar way to it working with DropBox. Being able to download books from my DropBox is one thing I really like about readers with a web browser. Note it usually works best to try the mobile site so for Box go to
https://m.box.com/ instead of the regular box.com