I decided to make my own system because none of the existing ones were what I personally wanted in a system. Simplistic (to a degree) mechanics, "grounded" combat that's dangerous and messy, focus on creative problem solving instead of just combat/etc, able to be used in any genre.
A lot of the challenges I encountered were when I was in relatively unexplored waters in terms of game mechanics. I'm not doing anything too out there, but it can be a bit of a hassle trying to figure out how well it all works together.
Perhaps both a challenge and an advantage, trying to create a system that was simple but also very grounded, Very minimalist "simulationist". Creating mechanics that were "realistic" was a bit hard, but also easy in the sense that I wasn't trying to create anything over the top, just find the best way to mimic real world rules.