The Custom Reports feature is good at mixing dimensions together (up to 3 levels of dimensions), but all the metrics available are mostly "Standard metrics" in Piwik and a custom report can only contain one of the 100+ metrics available by default in Piwik.
Custom Metrics are especially useful to process a "KPI" value for a given day or week or month. From user feedback:
An example of such a metric would be the ratio between successful vs. total searches or the monthly/weekly/daily active user count. We define active as done at least 1 search per week (a metric that could also change in the future).
Custom Metrics would let us create new custom metrics and generate a widget / report showing the value of the metric for the selected website and time period.