I will not talk about how awesome the campaign is, how cathartic the gameplay, how well paced, varied, balanced etc. This game plays extremely well and you should definitely try it out, but it's kind of boring to talk about just that.
No, let's talk about how subtle this game can be and how it deconstructs
general Transformers cliches without ever preaching, but through use of Sub Text
For example, Optimus Prime comes off as kind of a bloodlusty mass murderer imho. He kills without hesitation, sees every enemy not as a person but an obstacle or, even worse, some kind of pariah that has to be exterminated. Everyone who's not on his side is free to kill ("You chose the wrong side!"), he never really mourns that this war exists but only that HIS comrades die, and he doesn't even take prisoners. He basically wants to flee this planet because he thinks there's no hope for his Autobots left and only offers a truce once Megatron returns and the Autobots are in danger of losing again.
The Decepticons, on the other hand, come of as kind of cool guys. They honestly believe what they're doing is right, there's a clear "buddy dynamic" going on with the Combaticons, Megatron himself is much less of a Complete Monster
than usual. And, unlike the Autobots, they DO take prisoners. Megatrons inspires loyalty in his followers, talks about fighting honor a lot (which is fitting since he's a gladiator) and when he refuses Optimus' truce, it's probably because he sees the last Prime as a symbol of his oppression - and also a mass murderer who only wants peace once he's backed in a corner. And Megatron MAY be right with his "It's all your fault!"-rhetoric. Yeah, Megatron has started the war, but Optimus is way too eager to perpetuate it himself and kill any opposition there is.
In short, neither Autobots nor Decepticons come off as truly evil or heroic. The Autobots may have the moral highground, but that's not worth much when you're mercilessly killing hundreds of people while talking about "justice". The Decepticons on the other hand honestly believe what they're doing is a just cause - but they DID start this whole mess.
It's easy to see Fall of Cybertron as a complex study of war and how noone that participates in it can be seen as the clear good guy. Worth a thought. And worth your time and effort.