I faced the same dilemma, and eventually I went with the 2016 13" NTB. My reasoning:
- With $400 more I could have a quad core, 16 GB RAM, a bigger screen, and an Intel Iris Pro 5200. But then, I only plan to use it for Safari, Office 365, iTunes, PDF etc. and thus a quad core and a 16 GB RAM is kind off overkill. The Iris Pro 5200 is only slightly more powerful than the Iris 540, plus I don't plan to do any gaming on this - hence the point is irrelevant. A bigger screen is still nice, though, especially when I work in Excel.
- I don't need the SD card slot (not a photographer/video editor), have a wireless mouse, don't use the HDMI... essentially, I can live without USB-A ports. I still need to plug in my other Apple devices with the Mac though, such as iPhone and iPad, so I grabbed the USB-C to USB-A dongle for $7. The dongle will sit at home, so I don't have to carry it.
- I will miss the glowing Apple logo and MagSafe though, however, I think the new non-glowing logo matches the design of my iPad Air 2 and iPhone 6S.
- I will carry my machine daily, to work, to coffee etc. so lighter & thinner is a good think. I went to the Apple Store, and the 13" 2016 is HUGELY thinner and lighter compared to the 15" 2015. Again, portability is important to me.
- The 13" 2016 has some nice things such as louder speaker (which I don't need, since I plug my Mac into the external speakers at home anyways), faster SSD (I think it's not noticeable, the 15" 2015 is already unimaginably fast), brighter screen (I'll take it), and better battery life (important for portability). The only thing worse is the keyboard, it's noticebly louder, and I still prefer the old keyboard.
So in summary, I saved mysef $400 and got the 13" 2016. I'm an avid gamer, so I'm going to spend that $400 toward a new gaming desktop. So, a portable machine at work, and I come home to a beast at home, win-win for me.