I like mise a lot. As somewhat of a power user I've also found its rough edges though.
One is related to "change tracking" for tasks. Knowing when a task needs to run and when not based on inputs and outputs. I believe it uses mtimes and has somewhat similar problems in doing that reliably as make. For example, it would be nice if deleted files in output dirs would result in a task having to re-run.
Another is that I wish it was also a better task runner for long running foreground tasks. I've had to resort to pairing it up with pitchfork (by the same author but moreso an init system), overmind or hivemind. I think it should have the same set of options as pitchfork. And more controls around interrupt handling or setting delay/wait time after receiving an interrupt.