I am a former women's world champion who represented my state at the first national championship. I am also young, lower income, and living in a city with a skyrocketing cost of living. I qualify for the SCS every year by playing in tournaments that cost between $0 and $10, with few exceptions. My mission as someone who runs weekly $5 tournaments is to make competitive pinball motivating, exciting, and accessible to as many people as possible, and we see an average of 32 people each week. These are good, talented players, most of whom do not own their own pinball machines or travel to compete. The top 16 for my state includes a social services worker, a high school math teacher, multiple bartenders, two non-profit workers, and a literal child. I do not have the resources to pay a $125 lump sum at the beginning of the year, nor would I feel comfortable asking that of my player base. And I'm someone who only plays in the state I live in, so I'm not even part of the problem you're trying to solve!
I think many of the ideas proposed in this thread are meant to solve the very state-specific problems each poster experiences. Some states have one very powerful geographic area that shuts everyone else out. Some states host a major event that has outsized impact on the qualifying standings. Some states have people who compete in as many tournaments as humanly possible in order to qualify, rather than doing well in a few. In many cases, these suggestions are trying to solve problems that a) do not universally exist and b) may not actually have a statistically significant impact on the standings.
I hope that getting all these suggestions helps @pinwizj and the IFPA tweak things every year to get closer to an ideal system. I also hope that as these tweaks are made, the financial impact on individual players is considered. (And other things. This comment just happens to be focused on the monetary aspect.)