(IANA Astronomer) Each probe has a mission, and each instrument has an hypothesis it is designed to test -- that's the scientific method. Given the large fixed costs of space exploration, it's probably a better tradeoff for now to specialize fewer missions rather than risk gathering the same data hundreds of times over, while missing out on opportunities to test other hypotheses. (For example, I'm not sure what the benefit of 50 identical trips to the moon would be.)
Sure, we would learn a lot about managing a fleet of so many probes simultaneously (esp. when it comes to mission control, analyzing the data, etc), but those are operational concerns, which are orthogonal to the science they are trying to accomplish. And it's solving a non-issue: the only time we'll need to figure out to manage a fleet of probes is when we actually have a fleet of probes.
Sure, we would learn a lot about managing a fleet of so many probes simultaneously (esp. when it comes to mission control, analyzing the data, etc), but those are operational concerns, which are orthogonal to the science they are trying to accomplish. And it's solving a non-issue: the only time we'll need to figure out to manage a fleet of probes is when we actually have a fleet of probes.