Man of Steel definitely had less 'WTF?' moments plot-wise than Into Darkness.
Sorry, can't agree:
1) Kryptonians explored space for 100,000 years; yet when faced with the destruction of their world (and in this version no one disagrees with Jor El's assessment); can't/won't evacuate even though they are aware of plenty of habitable worlds in range? WTF?
2) Jor El owns/rides a 'flying dragon' (shades of 'Dragon Riders of Pern, or 'Avatar'.) WTF?
3) All Kryptonians are cloned (ala 'The Matrix'); and genetically designed to be the best at their assigned job/role/function. (This is a first for any version of the Superman mythos.) WTF?
4) The 'sacred Codex' (which is somehow the basis of all cloned Kryptonians); is a black, decaying and desiccated partial skull suspended in a laser beam. WTF?
5) When Clarks is talking to Johnathan Kent about the school bus incident, and Clark asks "Should I have let them die?" and Johnathan answers, "Yes, maybe..." (sorry but for me definitely WTF?
6) Johnathan dies because he doesn't want Clark going back out to save the family dog - and somehow risk exposing his powers to witnesses (even though if it did appear Clark was killed in that instance Clark could have easily come up with an explanation as to how he lived - and the dog wouldn't be able to tell ANYONE of Clark's powers...) WTF?
7) Kal El (aka Superman), who has spent his life avoiding fights, and was not trained to fight by anyone (least of all Johnathan Kent) can, somehow, defeat three kryptonian soldiers, and in the end General Zod himself (after Zod had acclimated to the Earth's atmosphere and his newfound abilities, including flight which he did in the final combat sequence) -- ALL of whom were genetically engineered as well as trained their entire lives to be nothing but combat soldiers...WTF?
Star Trek: Into Darkness:
1) For some reason Kirk decides to hide the U.S.S. Enterprise in the ocean of a primitive planet. WTF?
2) With 70+ odd genetically engineered 'supermen' in stasis; McCoy couldn't have removed one and used his blood to save Kirk? (Allowing Spock to kill Khan, etc if he so wished.) WTF?
3) The U.S. Enterprise can somehow be pulled/fall into Earth's gravity well/atmosphere 200,000+ miles from Earth (IE while in Lunar orbit.) WTF?
In the ST:ID story context as present, the above are pretty much all the major WTF?
moments that make little sense. Overall it's still about half (give or take) of the WTF?
moments in Man of Steel