The two movies are in completely different universes and a comparison is basically impossible. An important note though: In MOS, the speed of the Kryptonians isn't as great as many people think it is. In fact, it's definitely way less than the speed of sound, due to the fact that no glass breaks in the Smallville buildings only a few metres away from them when they move at their fastest. Furthermore, there isn't even a concussive wave heard or felt by their movement (all I heard was a punching sound at the end?), and it's clear they aren't teleporting, so they must be moving only at a fast car speed, unless all of the laws of physics are suddenly non-existent (I wouldn't even worry about this normally, but the MOS movie goes to extreme
lengths to try and convince the viewer it's being realistic, especially with the casualty toll in the final battle). None of the few people who survived in Smallville or Metropolis had shattered eardrums, IIRC. That level of speed is nothing spectacular, and it wouldn't decide any battle on its own.
By contrast, the MCU doesn't get so caught up in faux realism (thankfully), it just tones down a few of the powers when it needs to, while still making the heroes and villains something to be reckoned with, yet satisfyingly "super" enough to cheer for them. There are some inconsistencies introduced, but I find them relatively easy to stomach.
So which world/universe are the two fighting in? Once Superman...oops, er, Man of Steel
is in the MCU, all bets are off. And if Thor is in a DC movie, all bets are off.
In the end, it's all up to the writers, as I understood clearly way back when I saw a rogue Wasp take on all of the Avengers successfully (Hulk included). Whatever the story needs, that is what will happen.