Built-in EVF - Without saying, this is one of the features that make most people upgrade from existing NEX cameras. Basically, the EVF is one of the best on the market.
Programmable AEL button - This is the hallelujah feature for me because I use mostly manual focus lenses. I have assigned MF Assist to this button, which when pressed, will enlarge the view by 9.6x for easy focus fine tuning. My thumb no longer have to travel all the way down to the "C" button for this.
Electronic Level - Very handy feature for keeping the camera level. I have made a lot of use out of this feature.
Flat Camera Bottom - Can't tell you how much I hated the humped bottom of the NEX-5/5N. Can't mount the camera properly with that stupid hump.
Mode Dial - I don't change shooting mode that much, as it's usually set to "A", but I welcome this very convenient feature for the times that I need to shoot in other modes.
Standard Hot Shoe - Very handy to have when external flash, or wireless flash trigger is used.
Built-in Flash - I don't use it much, but could be useful for fill-flash in strong lights.
The Thumb Wheel - Excellent implementation and in the perfect place. This wheel allows me to change aperture or shutter speed with auto focus lenses. Sadly, it's pretty much useless when used with manual focus lenses, except when I shoot Shutter Speed Priority "S". Wish it can be re-programmed to exposure compensation.
That's about it. The new features of phase-detect focus, WiFi, User Installable Apps don't interest me much.
Hospital Entrance - NEX-6 & 16-50mm f3.5-5.6 OSS Lens. Click for larger.