Who cares if it's convenient? It's convenient that the Kent's family pet is trapped in a car during a tornado. It's convenient that the evil Kryptonian's arrive as soon as Superman emerges. It's convenient that Jack Napier is the killer of Bruce Wayne's parents. It's convenient that Bruce Wayne is trained by an evil terrorist organization. It's convenient that Peter Parker and Norman Osborn get their powers on the same night. It's convenient that Peter loses his powers right when Doc Ock shows up.
It's set up in the beginning of the film that Jor-El and Krypton has sentenced the three villains to a life of prison in the Phantom Zone. That's enough for me. Atleast the filmmakers and writers carefully set it up.
Jor-El warns Clark that there may be a day that he may have to face Zod. It's all set up perfectly and shows Superman's hubris and selfishness. If he hadn't focused all his efforts on one person (Lois) he wouldn't have,
- freed Zod and Co.
- lost his powers while Zod and Co. terrorize the planet
Superman comes out of that a stronger character, "sorry I've been away so long, I'll never let you down again". Hell, he even realizes his folly after he's beaten to a pulp by the trucker at the diner.
What are the chances that a tornado shows up in Kansas?
Compared to the chances of a meandering mirror in space on god knows how far Krypton is from earth, but far enough that you need to bend space to get there, to arrive at the exact moment when the nuke is being thrown directly at it?
And every other case you mentioned is highly more likely that that.
And again, that doesn't set up that he can save everybody, in fact, he can't, that's why he had to reverse time.
Also, the fact that Zod arrived in MoS wasn't convenient, did you miss the part where Supes actually sends a signal by starting his ship?
It's physically impossible (as far as we know) to turn back time by flying around the earth as fast as we possibly can.
But you know what? It's physically impossible for a humanoid with a mass like Superman to be able to fly. Or lift tons and tons over your own weight. Or shoot rays from his eyes. Or change clothes in the blink of an eye. Or have a magical crystal fortress full of weird, magical ****. Or have your dad's consciousness talk to you in full form, floating around in said fortress after being dead for years. Or have skin and clothes that are resistant to wounds or tears. It's impossible to kiss a chick and make her forget everything. It's impossible to literally split into two people. There are no physics to Superman.
Turning back time is just as natural as any of the crazy crap he does that doesn't physically make sense in comics or movies.
It was only a matter of time before the excuse: "So what if he can reverse the time? he can also fliez! Iz both impozibles!!!
Not only it's impossible to reverse time like that, Do you have any idea of how fast the Earth rotates? If you simply reduce the rotation speed a little, ALL of us, and all things not attached to earth would be victim of inertia, now imagine stopping... now imagine REVERSING, instantly, Every living thing would die, talk about saving everyone
Now, regarding the flight, there are several theories: Controlling his own gravitational field is one of them, that's no impossible, there are several theories of anti gravity devices, a feat of strength, compressing the air so hard and so fast that it turns into a solid platform.
Almost indestructible clothing, why not? You know how resistant graphene is? Who's to say an Alien technology can't achieve more?
Impenetrable skin, that's perfectly explained.
Heat vision, could be a mutation.
None of Superman traits actually break any rules of science or science fiction, not at least in the distance STMP did.
