Nexus is the main reason:
Pure Android, no bloatware, no "skins" (skins is a mislabel for touchwiz, etc)
Fastest upgrades to software versions
Much longer support to new software versions
Updates directly from Google, rather than reliant on carriers
Storage is a problem, just like on the DNA
No annoying physical buttons and/or carrier logos
Price (starting $200 below other phones of it's class)
No Contract Required
Personally I can't stand the Touchwiz, Sense, etc. and buying the hardware and flashing a stock rom tends to cause you to lose many of the selling features of the phones that build that functionality into their software, not into flashable apps. I honestly feel the hardware is better in the Nexus than both the DNA and the S3 (except removable SD card in the S3 and screen on the DNA), but the Note 2 is obviously the best of all 4 in terms of hardware. If you remove Samsung's software from the Note, it loses the majority of it's selling features, which to me puts it equal to the Nexus 4, but 2x the price. Best value by far then, becomes the Nexus 4.