For example, in response to the latest security hullabaloo, we recently added a Nagios check for libc being too old, and for running processes that are linked to a libc older than the one on disk. This isn't a time series check; it's just an alert condition. Polling for that alert condition isn't what Prometheus is going to be good at, so cramming it into that alert pipeline is awkward. If we used something like Prometheus, we'd have rules in two places already.
Polling prometheus for saved queries and simply alerting on a threshold might result in a simpler system. The rules that could be expressed in an alert pipeline could be expressed as different queries, and all rules about thresholds, alerting or notifications could be done further down the pipeline. There's still some logic about what you're measuring in Prometheus, but not about what thresholds are alerts, or when, or for how long, or who cares. Threshold rules could all live in one place.
This isn't a knock on Prometheus, which of course supports a workflow along those lines, and seems interesting. Nor is it a knock on the prometheus alert system. I just wonder why software in the monitoring/notification/alerting space always ends up muddy. I believe the overlapping boundaries between projects are a symptom, not a cause. I keep asking myself if there's some fundamental complexity that I'm not yet appreciating.