I honestly think they made a mistake making Zod and crew the villians. It brought far more attention to the nature of Superman's powers than was really necessary, or even wise.
Lower gravity. a different atmosphere, and yellow sunlight lets you freakin' fly and shoot lasers out of your eyes? And all of those abilities just magically disappear the minute you start breathing your own planet's air again?
Ummm... What?
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Call me a stickler for supension of disbelief, but if your premise makes that little sense, the last thing you want to do is explicitly invite the audience to analyze it deeper.
The simple fact of the matter is that no one really gives a damn how Superman's powers work at this point. It's just kind of accepted that they do. They didn't need to reinvent the wheel.
I think Brainiac would've been a smarter choice. That way they could've avoided those kinds of questions while keeping the alien invasion angle and the Kryptonian technology.