For one, from what I understand, Ninjablocks connects sensors to your network via ethernet or wifi. In practice, that's a bad way to do home automation. It looks like SmartThings is using a mesh network (Zigbee or Zwave), which is way more scalable and self-extends its range as you add more devices to the mesh. Using Zigbee/Zwave and Bluetooth 4.0 also means sensors can be super low power... just pop a battery in a sensor and stick it somewhere and have it last for years before needing to replace the battery. Ninjablocks can't do that. Devices that connect via ethernet/wifi/usb are a lot more demanding power-wise.
Also, NinjaBlocks is all about having sensors trigger online actions. That's cool, but what if I want it to trigger my door to unlock? They allude to being able to do that in the future, but from what I gather it will on their site you'll have to cobble together a DIY solution yourself.