> How do you change the markup language to be consistent between Jira and Confluence?

This here is the single most insane thing about Atlassian.

> allow any ticket to be a child of any other ticket?

I have no idea why you would want this from a work management point of view, but you can just use issue linking to describe a parent <-> child relationship.

Re 1: I'm not sure why that's a necessity beyond a notion of consistency. I find that major wiki editors are not often major ticket creators, and these are different products with different audiences at the end of the day. Also, Confluence uses a WYSIWYG editor, so it's rare to need to think about the markup.

Re 2: Set the project's issue type scheme to one that only allows tasks and subtasks. That gets you one level of nesting. (And even though task and subtasks are different issue types, changing from one to the other is trivial since they have identical fields.) Allowing epics gets you another at the top level. That's a bit limited, but wouldn't arbitrary nesting be even more complex?