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I don't quite understand the breathing issues Superman had on Zod's ship. Specifically in the context of the fact that he doesn't strictly need to breath to stay alive. This is shown when they were at the satellite, or Superman staying submerged under water for an undetermined amount of time.
So, why then did he have problems on Zod's ship, when in these other cases he didn't need to breath at all?
This is Nolan's way of including Superman's weakness - Kryptonite. Instead of saying that one material from Krypton affects him, this is a better explanation or design. The planet itself is alien to Kal since he has been inhibiting Earth for 33 years. So when the environment changes he gets affected by it.
Breathing was not the issue at all, pretty much everything is. The visual way of showing it was his loss in strength, coughing and stumbling.
One explanation can be stated as a matter of adaptivity.
We can assume that Superman has been in space a few times before this fight. Even though he just 'gained' his flight ability, he was still used to the lack of atmosphere in space before the fights.
Flash ahead to Zod's ship where the atmosphere is the exact replica of Krypton's, something Kal'El is obviously not used to at all and is apparently very hindering to the physiology of the Kryptonians. Kal, not being used to this atmosphere as well as its sudden hindering effect on him causes a slight reaction that doesn't mix well for some time.
I imagined this very simply, if the atmosphere on Earth is much richer than that of Kryton (and grants him his powers) he's adapted to be used to it. However, if you take him and put him back on Krypton then he wouldn't be used to having such little sustenance from the air.
Consider it like altitude sickness, many athletes train at high altitudes so they can exploit the extra oxygen when they race at sea level. Superman is used to training at sea level so if you take him to the top of a mountain there's much less oxygen (or whatever he's drawing power from) than he's used to.
Eventually does adapt but it takes a little time and he's not got his powers.
As per Jor-El's comparison of Kryptonian and Earth conditions, Earth was more welcoming to life and was said to nourish and ecourage it. While Krypton was "hard" on life.
Breathing is a part of the process where the body gets power to sustain itself. In case of Kal-El, he also has the sun. So he may survive for some time outside of an atmosphere where the sun is present. Whereas on the craft, the kryptonian atmosphere acted like a poison to his body, because of it's harsh nature.
Also, Kal-El was barely able to accept and comprehend the immense power he posses due to being on Earth. So also at a mental level, this is something totally new to his body. On earth, he lived as a superbeing, not being affected by sickness, tiredness and other ailments.
Clark has never been around kryptonian atmosphere before as Zod said that he has spent a lifetime adapting to Earth's ecology that he never adapted to theirs.
