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.
The hurdles aren't natural, they are human-made constructs.