I’d argue it’s man against nature in its rawest form. Many sci fi films try to use this as a plot point (“I know the math, punch it” in Iron man for example), but GATTACA handles it head on - the protagonist battling what’s supposedly his nature given limitations is what I would consider the main if not only quality that makes man “not natural” more so than even any artificial intelligence we may create tomorrow.
He's not battling his natural limitations. He's battling the genetic-discrimination-based oppression imposed by society: the police who will use force to stop him from doing the things of which he is naturally capable.
The hurdles aren't natural, they are human-made constructs.
I think it's at least strongly implied in the movie that he has to work much harder than (for example) his genetically superior brother to achieve the same level of performance. So maybe you're both right.
From the point of view of the Space Agency even though his ‘spot’ performance meets the grade he’s still an unacceptable risk as an astronaut - he might die during a mission potentially harming others - and if so all the resources spent on that mission and training would have been wasted.
In a sense it’s the external political struggle of whether a society allocates resources to everyone to maximise their personal potential, or focuses resources on a subset of talented individuals likely to give the best overall return.
