On the MUX, the Senate wasn't as universally corrupt or powerful as it was in IDW. It was a long-lasting body that waxed and waned in power, and included members as dastardly, heroic, or both, as any real world institution. Towards the end it was widely distrusted, making it easy for the Decepticons to whip up propaganda against them, but the association of "Senate = All-Powerful Evil" is an untrue oversimplification on the MUX.
As Megatron Origin was based on the decline of the Roman Empire, the Senate was most likely based on the Roman Senate. Unlike that Senate, according to Optimus, they're not made up of former magistrates but of the descendants of the Progenitors, i.e. they inherit their seats.
Origin presented the Senate as meeting in Kaon, and in the same bloody prison building the Decepticons are in.
The thinking by James Roberts is that by Nominus Prime's time, the Primes had become a less powerful force absorbed into the Senate, rather like the British Royal Family. The Senate itself, as partly established in flashback stories, is increasingly factionalised body with groups fighting each other out and shifting their allegiances. (AKA, a senate) 
Chris Metzen's intention was that nobody knew precisely who killed the old Senate as the Decepticons had suppressed the footage and Starscream wasn't known to be a Decepticon, hence him appearing as a delegate. This was proven even further in Optimus Prime #3 when Soundwave noted that there existed no recorded evidence to prove exactly who was responsible for the Senate's death.