The upside inherent in fifty parallel and bespoke experiments in government is worth the extra complexity and cost. Ideas are tried out, and can bubble outward and upward if they work. Bad ideas directly impact only ~2% of the country.
Furthermore, having state and local control over elections has a direct impact on legitimacy. I don't have to believe that someone in Washington DC is doing things right. Instead, I can interact directly with our state's secretary of state and our local county elections office.
Decentralization with heterogeneous procedures makes election compromise a much greater logistical challenge for any nefarious actor. It is probably a lot easier to spend money on lobbying.
Edit: Finally -- if you want your local/state elections infrastructure to have more resources, your voice and your vote are your tools.