I think the reason the TFA writers made UM the Supreme Commander of the Autobots so they could have a morally......."adjustive" leader. -In Mission Accomplished, he states that they (the Elite Guard and Optimus's crew) must lie to their fellow Autobots regarding Megatron's fate and the shattering of the AllSpark. -In Rise of Safeguard, he states he can't "waste" Elite Guard resources on the project. -And finally, in the flashback showing Omega's construction, he says "We're at war, soldier....we do what we must.", referring to creating sentient WMD with limited mental capacity, so it can't consider the implications of its acts. When you think about it, they couldn't do this with Optimus Prime, because Prime is meant to be the paragon of virtue, but with Ultra Magnus, we have a character leading the Autobots who will cross the line to get the job done.