I find that Dune works pretty well for basic cases, but I am occasionally frustrated by portions of its interface that don’t anticipate simple variations to common workflows.
One of my recent posts provides an example of a workflow squarely within “the OCaml niche” that seems like it should be trivial, and probably would be trivial with a traditional build system. (I’m still looking for a solution, by the way. 
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I do wish there were a larger middle ground between the chaotic, shell-driven workflows of Make and the clean-but-austere approach of Dune stanzas. The auxiliary Dune Libraries seem like a promising start (I found the Configurator easy to use), and I hope we’ll see more extension points like these in the future. Are there any plans @rgrinberg ?