Museo Memoria y Tolerancia is one of Mexico City's most serious museums, using genocide, discrimination, and human rights abuses to ask how societies learn to live with difference. The subject matter is heavy, but the museum is carefully presented and sits right beside Alameda Central, making it easy to fold into a Centro Histórico day.
Allow more time than you think. The best visit is slow, with a break afterwards in the park or at a nearby cafe rather than rushing straight into the next sight.