Both recorders have 7" monitors and are capable of recording 4K ProRes and Avid DNxHR. The only real difference between the two is the Ninja Assassin is HDMI only, while the Shogun has 6G-SDI in addition to HDMI. Here's a look at the price cuts on both models:

Atomos Shogun - Ninja Assassin Price Drop

Atomos has extended the functionality of their recorders significantly in the last few months with their 6.5 firmware. In future updates hopefully coming in the first half of this year, they will be able to record RAW directly to CinemaDNG from Sony, Canon, and ARRI cameras:

You can also get a free CFast card when you buy one of their tiny 1080p Ninja Star ProRes recorders:

Atomos Ninja Assassin — B&H

Atomos Shogun — B&H

Atomos Ninja Star — B&H