Consider for a moment what it would mean for the omniscient creator of the universe to design a system for living for the denizens of the universe. As I think of it, the system would be perfectly in tune with the way the universe works on a standard basis. Everything the people of the universe would come in contact with would fit perfectly into roles and categories designed by the omniscient creator and there would be no grey areas. Things would always work out. See, if the universe, people and the rules for people in the universe to live by were all composed by the same omniscient source, we should not expect any contradictions or problems between what the rules order and what reality is, right?
For example, if such a creator were to design a system that differentiates between men and women, and differentiates strongly at that, I would think the way of the universe would never allow for some grey area where the individual could be neither a male or female or both male and female, right? The situation should simply never come up. And yet it does. While relatively rare, individuals are born with intersexual anatomies that run the entire gamut between male and female. It is even possible, and cases have been documented, that a person can be born with one testes and one ovary.
If prayers were supposed to be given every day at specific times of the day depending on the placement of the Sun in the sky during the course of the day then I would think that there could never be a situation where a person could be living in a place where such a system wasn't in effect. Yet there are such places. At the higher latitudes there can be instances where the Sun doesn't set for six months or alternatively when it doesn't rise for six months. And then of course there is all that space outside of the Earth where one may not experience any sort of planetary revolution at all.
The point I'm making about all of this is that Halacha has certain assumptions built into it regarding the way of the world that never would have been assumed by the omniscient creator. If God was writing Halacha or otherwise ensuring its correctness through the ages it would never have these categorical errors in the first place. Prayer times would never have been defined by the position of the Sun because that's only useful in special cases. And otherwise, if the system required male or female in black and white terms, the world would not be designed in such a way that male and female status could be unclear. If God is the creator of both the world and Halacha then there should not be this disconnect which seems exactly like humans took their false or biased understanding of the world and built a legal system around that impression.
Now, of course, there are Halachic 'patches' for these and similar issues. If you go to the North Pole just follow the zmanim you would from where you come from. But this misses the point. You don't need patches on a perfect system. The point again is that these are categorical misapprehensions of the way the world works. Something an omniscient creator could never have done.