I thought MOS was better by miles. One thing I thought of, in STM, Lois sees Clark running past the train. Even if she is a little young, how does she not years later when SM shows up be like "this must have been that boy I saw running on the train as a child just outside Smallville. Wait, Clark is from Smallville." At least she should think along these lines.
I loved Lois Lane way more in MOS. She was a good reporter, not a reporter who could not spell, and not see what was in front of her that we are told is good.
Also, in STM, the success of Luthor's plot relies on everyone else being very incompetent at points. In MOS, Superman has to use all his effort and energy just to stop the World Engine.
Lastly, if Clark can move fast enough to turn back time, why can't he move fast enough to intercept both missiles?