Okay, the Dinobots. I get it, Shockwave got their design from our planet, he studied the earth, it's all explained. No problem's here. However... Why does he CALL them "Dinobots"? Where did he get that name? I mean, he doesn't know we humans will call these animals "dinosaurs", now does he?
I'd chalk it up to translating from Cybertronian to English. Also, in some comics, the team is known as the Dynabots, as in dynamite or dynamic, which sounds similar.
Why does Starscream outrank Onslaught and Shockwave? I know Megatron isn't the most rational thinker, but why make the worst possible choice to rank above the more practical ones?
Keep your friends close, and your enemies closer.
Why is Megatron so mad seeing Starscream as leader when he's Back from the Dead? We already saw that he knew he wanted to overthrow him, so why is when he sees him acting exactly the way he knew he would act?
It probably had something to do with Starscream talking about "Gone are the failures of Megatron!" and trying to turn the Decepticons against Megatron.
Why was Metroplex made? Trypticon was made out of a Kill Sat the decepticons came up with. Omega Supreme already had a good reason (Being the gatekeeper and whatnot). What's the point of Metroplex?
He responds to the will of the Primes. Perhaps he was originally a weapon, built during the early days of Cybertron then forgotten.
On Bumblebee's mission, a tentacle from the Nemesis shatters a window on the Ark and all the Autobot redshirts get sucked out (indicating that the Ark is pressurized), leaving only Bumblebee. Ratchet immediately swears that they will be avenged. This brings up two questions since it is firmly established that Cybertronians can survive in the vacuum of space (as demonstrated by Bumblebee himself later in the very same mission). First, why would the Ark need to be pressurized when Cybertronians don't breathe? Second, why does Ratchet react as if the redshirts were killed by being sucked out when they can survive in the vacuum of space?
Atmosphere might have alternate functions, like insulation, and not having to breathe might make their fate all the worse, because without some means of getting back, they're kind of stuck in the void of space.
Why didn't Optimus just have Metroplex crush Starscream and Soundwave for a fuller decapitation strike?
Because it's Optimus Prime. He can't not give the Decepticons a chance to leave peacefully. Megatron's death was the only option, as far as he saw.
That, and the fact that if he killed off Starscream, Onslaught, and Soundwave, Shockwave or someone else less predictable would take over. Better the devil you know than the devil you don't know. One of the Decepticon mooks later in Cliffjumper's level remarks that he's more comfortable with Starscream rather than Shockwave as leader, since Shockwave is considered a nutjob by many 'Cons who don't understand him.