It seems that so so many tools can't properly handle a good work breakdown structure - you can break your tasks down, but some arbitrary level of work (usually first or second tier tasks) is the atomic unit of work for a sprint.
I'm looking for Kanban, sub projects, hierarchical tasks, control over estimating, and not much else.
The critical function that none of the software I'm looking at can really do is putting a single sub-task from a story into a sprint.
The reason you're not finding this function is that it's in contradiction to agile/scrum technique. A sprint is a commitment to finish a set of stories in a time period. It doesn't make sense to take a sub-task of a story and put it into a sprint -- either you finished the work you committed to or you didn't, and if not, you should let the fact that you weren't able to finish it adjust your velocity for the next sprint.
You could make your story into an epic, and your sub-tasks into stories.
Pivotal Tracker (cloud-hosted), JIRA (cloud-hosted) and taiga.io (open source, self-hosted) are the best tools I've used.