The casting of Peter Weller as Admiral Marcus won a lot of points with me, the guy can do no wrong in my book and he was brilliant in this, just like he was in the two part Star Trek: Enterprise episodes Demons and Terra Prime. Saying that, there were a couple of things about his character that bothered me.
Marcus is a top level Admiral in Starfleet and also the man responsible for using Khan to design advanced weaponry. He is worried that Earth is not defended properly and that he is the only one who is taking the danger seriously. The Klingons are on Starfleets doorstep and Marcus feels that the organisation is under prepared. So that is why he forces Khan to work for him while holding 72 of Khans people as frozen hostages. He needed Khans aggression and superior mind to produce superior weaponry so Khan helps him build the USS Vengeance, a beast of a starship designed purely to fight.
You can believe that the Admiral deeply cares about Earth and its people, which is what motivates him to go behind Starfleets back. A misguided hero who feels his short-term unethical actions will secure Earths long-term future. But when he turns into a full on bad guy, then his character starts to make no sense.
Firstly he is prepared to start a war with the Klingons. He wants the Enterprise to fire the 72 advanced torpedoes that contain Khans people at the Klingon home world. Not only will it deal with the Khan issue but it would also make the Klingons think that Starfleet launch a preemptive strike on the Klingon home world. He also arranged for the Enterprise to break down in Klingon space so that the Klingons would find the Enterprise and destroy her. Admiral Marcus would have tied up all the loose ends, be free to make up whatever story he wanted and save his own ass.
But for a man who is going to such lengths to make sure Earth is safe, what would starting a fight with the Klingons actually achieve? If he thinks that Starfleet is not ready and he only has one Dreadnought Class starship, the USS Vengeance, isnt he just asking for trouble?
Later in the film, Admiral Marcus takes the USS Vengeance to destroy the Enterprise. After a short fight near the moon, the Enterprise is crippled and Kirk pleads with Marcus to spare the crews life. But now that Marcus is the movies bad guy, he coldly thanks Kirk for the offer but informs him that he has no intention of sparing the Enterprise or its crew. Has he always been a mass murdering psychopath? There is no regret in his action, he is almost relishing seeing hundreds of innocent people die. Where have his Starfleet ethics gone?
There must be something in the Replicators on the Vengeance because Admiral Marcus is not the only murdering nut job on the ship. The USS Vengeances human crew are also happy to have the blood of innocents on their hands. Identified by Scotty as private security, we are supposed to believe that Admiral Marcus has hired this group of people and they will do whatever he asks, even kill a starship full of people. Do they work for Starfleet? Are they part of Section 31? Who are they and why are they blindly doing whatever Admiral Marcus orders?
Also, how exactly has Admiral Marcus managed to hide Khan and build the USS Vengeance within the Solar System without the rest of Starfleet finding out what he is doing? Its not like his facility around Jupiter has top-notch security, Scotty managed to enter the facility in a Shuttlecraft without being detected. Scotty even managed to disable the USS Vengeance and make unauthorised communications to the Enterprise without the Vengeance internal sensors picking it up.
Towards the end of the film, Admiral Marcus is all over the place, his character starts to make less and less sense. On one hand he keeps talking about how he is the only one who can save Earth but on the other hand, the only people he seems to care about are himself and his daughter. How did a psycho like this make it to the rank of Admiral?
And the fight between the Enterprise and the Vengeance that takes place near Earth. Where are the other Starfleet ships? Why is no one concerned that there is a fight going on near the Moon? Why is no one in Starfleet command wondering where the USS Vengeance came from? The fight is taking place near Earth and you dont even see a Shuttlecraft come up and have a look.
There were a couple of unintentional comedy moments in the scenes on the Vengeance. The security guard that catches Scotty messing around with the airlock controls must go down as the worst security guard in the history of Star Trek. He just stands there pointing his phaser at Scotty and asking him what are you doing? Even when he hears Uhura talking over the communicator, he still just stands there and does nothing.
The second bit I found it hilarious was when Kirk confronts Marcus on the bridge of the Vengeance. Kirk and Khan have stunned/killed all of the Vengeance crew but for some reason, Kirk wont stun Admiral Marcus in front of his daughter in case it upsets her. Why not? Are the feelings of Carol Marcus so important that Kirk will risk the safety of the rest of the crew? Just silliness and more bad script writing.