For me, it's the internal memory. Coming from the EVO 4G, the measly 400+ MB in usable memory became the bane of my existence, constantly having to manage memory, delete apps and clear cache. So for a new phone, I wanted it to be more future proof in terms of ROM.
The new EVO is appealing because of the 1.5 DC processor (versus 1.2 on GN) and the gorilla glass etc (I also love the heftier weight), but it only comes with 16 GB ROM (versus 32 on GN) and although it does allow an SD card, we all know many apps still don't save to SD. The GN does not allows an SD card, but I feel fine knowing I have 32 GB's to work with right off the bat.
The inability to remove the battery is an issue too, as my EVO 4G REQUIRED a 2nd battery, especially when I was traveling. Not being able to swap the battery on the go if I'm running out of juice is a HUGE negative.
Lastly, the pure Google experience is wonderful. When I got my Nexus, I LOVED that there was ZERO Sprint bloatware on the device. I even had to install Flash, because it didn't come standard and allowed the user to decide exactly what they wanted to take up space. On my EVO, apps like Facebook came installed and could never be fully uninstalled, only the updates. The lack of NASCAR and Blockbuster junk on the phone is fantastic!
My gripes with the Nexus are that there is no easy way to make a song your ringtone without
transferring the file to a folder (versus a simple long press or settings option on HTC) and I am not a fan of the Samsung ringer and sound options. Also, there is no visual voicemail, so I had to get a 3rd party app (YouMail) to cover that. There are a few other niggling issues, but nothing worth writing about as a major negative.