Allow the ability to add hash marks to the parent time bar in Gantt based on child dates. This would allow to see milestones without cluttering the view with multiple child issues.

I know it's not likely that you can interface with every other add-on that structure customers might also use, but selfishly, I would love to be able to view all test cases associated with an issue under that issue (similar to Extend with linked issue).

Add a count of the number of comments.

This idea is a to provide a way to display only (or to hide) some fixVersion instead off all of them when we use the grouping feature. If it is possible to choose the storing order (asc, dsc) it would be awesome !

These fields are of extreme importance for time management throughout the project.

I'd like to see my dates roll up the hierarchy so that I can see higher level estimates as they roll up. For example, if I have a folder for a project and I have a number of tasks underneath, I'd like to see the latest due date in the project, or the earliest start date.

As a gantt user, I would like to get my the release date of my versions automatically projected as milestones on the timeline, so that when I bind a task to it, it automatically update the fix version/s field.

I would suggest you to resort exclusively to the AUI objects for your interface instead of your custom ones that clearly gives the impression that you are exiting the Jira world to step into another one.
I think you user would deserve a smoother user experience, with the same kind of buttons, icons, tables to which they are already used to. I'm especially talking about the transformation/filters features that should be improved in that direction to my mind. Thanks for you great achievement!

Budgets are often not added as issues. Structure could add value by allowing some limited amount of named custom fields on structure-folders (like notes, but some more). They would bind to a structure and could be accessed from formula columns.

The Structure 4.5 documentation doesn't identify how to create a NEW Formula Column.
https://wiki.almworks.com/display/structure/Formula+Column

Step 1 should identify how to add a new field, not how to write the formula.

I assume a lot of people want to use structure for reporting as well. Most teams work with sprints and therefore it is essential to be able to select "sprints" as a filter for worklogs in structure views. A structure/or view could show worklogs for a certain sprint only and besides also for the involved team as well

when you report worklogs with structure, you want to use the worklog column and specify a time period.
If you add multiple columns, it is quite an effort to change the time period from eg. dates of jan to feb. (currentmonth is helpful, but somewhat too dynamic if you want to compare months)

To easily switch between months it is necessary to switch the time period you look on on the view level and influence alle worklog columns this way.

E.g. to calculate a percentual distribution over all rows of a structure, for the formula you need the 100% value which is typically shown on the root element.

Therefore it would make a lot of sense, to be able inside "formula column A" to use a columns B's value, but the root element value! This should be possible even if column B is a formula itself.
As we can already use variables like "Column B ..." in formulas it would be nice to add "Root Value of Column B ..." to the variable selection list

The Structure 4.5 documentation is lacking when describing how to create new views.

For example, if I take "Basic View" and copy it to my Structure, I would expect that I could edit it, but the View Details screen says

Access: Use - you can use this view but you cannot update it.

There is no "Save As" button as indicated by the documentation.

Require the user to confirm a deletion of an issue before it is removed from the structure. Right now there is a message that an issue has been deleted, but my users aren't noticing the message. Need to make them verify the deletion before it will occur.

I create some rather large Structure charts with multiple levels of nesting. Want to be able to highlight aspects of the chart (Rows, Cells, Columns) with color. This helps with focus (these items are critical), organization and overall visual appeal.

When an issue appears multiple times in a structure (e.g. epic link and issue link),the progress calculation should be configurable to prevent / allow double counting

Structure formulas are extremely useful. Now our users would like ways of using them in other places within Jira. This may be tough in some ways because they are specific to the structure they are part of, but even something simple like the ability to choose an menu option or call some API to commit formulas into an underlying custom field could be quite useful.