Guessing it was either a hit tip to the original comics or movies or foreshadowing the sequel.

One obvious way would be to make any attempt at all to take his superpowered beatdowns away from a populace that was constantly in danger. OR I'll do you one better, rather than take the fight away from civilians, how about don't willfully drag the bad guys to the most populated area around (Main Street Smallville) for the fight in the first place.

Another one, and this was just a plot head-scratcher, Have the military deal with the world machine since all it apparently took was him flying through it to destroy it. I have a hard time believing the entire might of the worlds military couldn't have dealt with that. This would leave Superman to deal with the much more pressing matter of conservatively 10's of thousands of people dying in Metropolis. (Not to mention all the people flying a suicide mission to deliver his escape pod rather than him just doing it himself faster than the speed of sound)

Also, if the argument is he isn't Superman yet, fine. I disagree with that rationale, but fine. Then who IS he? I had no idea by the end of the film. I saw practically no defining traits or genuinely human moments from him (or practically anyone else in the film). He was a cardboard cut out.

Why exactly did Lois get put into a room that had potential access to the entire mainframe of the ship? Didnt make much sense.

Because they didn't know she had a key that would allow her to use it. Why would they?

Regardless, just because I have you handcuffed and blindfolded, doesnt mean I am going to throw you in a bank vault filled with gold. Was a weak plot thread to get her off the ship

Wait, so you'd rather have the climax of the movie in the middle of the desert or something? What exactly was he supposed to do? Drag Zod there or something?

that kind of bugged me too. But one way I reconciled it was to assume those key things were in every room

This. The fight was where Zod deemed it to be. He wanted to make Superman chose. It was stop them or let more people die. Any moment he would've taken away from the fight to save someone hundreds others would have died. Zod's Commander chick even said as much in the movie. "For everyone one you save we will kill hundreds." or something like that.