What makes you say that? Most accidents are driver error. The stats show that CDL drivers, who undergo more stringent testing, have a lower accident rate than others.
"Engineer them for safety rather than traffic throughput."
What would that look like? Even if you replace stop signs with roundabouts, the drivers still need knowledge of how to safely navigate them. If you're talking about reducing speed (technically the most effect if enforced systematically), how do we ensure enforcement?