I'm having the same issue. And "Milestones" would be the way to go. However they do not appear in reports so it seems it's not yet fully functional yet.
However please note that Flow outcomes/milestones is focused on "Self help" not true IVR reporting. So you might not get what you looking for later on.
Your best bet would be to set Attributes on the call within the flow and make a custom report. But if you don't want to customize you could always just update a table when a call passes by a menu choice. One row per menu option and then do a +1 or add a timestamp.
I would advice to have a look at the ideas site to ask Genesys for this functionality.
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Andrew Lagarde
KPN B.V.
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