Snyder not only makes style-over-substance films, but he also distorts or destroys the source material's intent. Superman in Man of Steel is a good guy for reasons not shown in the film. Watchmen is a 3+ hour long music video without any of the biting commentary of the original comics.
Someone explain to me why he is a good filmmaker.
So I decided to give MoS a shot - I'd rate it a C+ but not so much for the reasons you mentioned. The film did have a fair share of plot-holes such as:
*Zod is a terrible general - he shows up on a plant of 7 billion people with an "army" of about 12 henchmen - and his first instinct is to just threaten loudly that he's gonna destroy the world instead of negotiating? (Not to mention that they didn't even have full superhuman powers when they first arrived on earth) Even if Superman wasn't there to save the day, the military couldn't just nuked Zod's group into oblivion once things got too hot and heavy.
*The romance between Lois and Superman was very rushed - he wasn't even working at the Daily Planet when they first met, and they'd only met twice on-screen before the entire Zod incident went down. And what about Lana? They showed her a few times in the flashbacks and then she's never heard from again.
*The "humans don't trust Superman" thing felt like it was forced into the film more than anything - I mean, the soldiers know the Kryptonians are strong enough to take down A-10 Warthogs with their bare hands, yet they decide to fire at Superman anyway knowing he's the only one strong enough to fight them?
*The film had a couple awful lines - for example when Zod's henchwoman tells Superman that they're stronger than him because they have no 'morality'. Since when do villains "admit they've evil" outside of Saturday morning cartoons? Not to mention Zod goes off on several rants about how he's supposedly doing it 'for the greater good' of the Kryptonians. So basically this line is like the villains saying "Oh all that stuff we said about the greater good of Krypton is ******** - we're really just evil comic book bad guys who love killing people".
*How did Clark find the fortress of Solitude anyway?
*The flashback scene where Superman destroys the drunk *******'s truck is pretty crazy. I mean, Superman decides not to punch him to avoid giving his powers away - and decides that tearing up a semi truck with his bare hands is more descreet? The guy is going to know that if anyone did it it was Clark, and Clark works at the diner - so when the police investigate it he's going to become a suspect sooner or later. If he wanted to be discreet, he could've just crushed a beer bottle with his bare hands and told the guy he was a 3rd degree black belt in Jiu Jitsu, or something.
*They also need a better explanation for Clark keeping his identity a secret other than the glasses - in the 21st century with smartphones, mass media, and Google, someone somewhere besides Lois is going to recognize him as Superman. If they make a sequel, they could ret-con it so that Superman's suit has a technology that makes his face unrecognizable to humans while wearing it - or something.
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*After seeing it though, I think the gripes you have about Supes siding with the humans aren't the biggest faults of the movie. Even if his earth father told him not to trust humans, he still had met his Krypton father in a vision who told him his purpose for him was to be a hero to earth; not to mention Superman knew that Zod had murdered his real father, and tried to harm his mother - so why would Superman side with his father's killer anyway? If nothing else, siding with the humans just to get revenge on Zod still would've made a lot more sense than siding with Zod. The tone also wasn't nearly as bleak and gritty as The Dark Knight - it wasn't as light-hearted as a lot of the Marvel flicks, but other than using the same color scheme, it wasn't nearly comparable.