First of all the information presented when you get to Node Permissions is quite lacking. It only indicates whether any one group has changed permissions. It doesn't say whether registered users have access to view the node.
Once you click on the node, the information you get about the usergroups permission is also lacking. And making changes to numerous usergroups is laborious in the sense that only one usergroup can be viewed/changed at a time.
There is no way to quickly change settings to revoke access, or revert to default, possibly the most commonly used actions. So you have to click through each usergroup (40) and change the permission for each node (I have 600, about 100 of them are unique to the node).
Once you go to the usergroup permission to that node (not to be confused with the Group Info on the right), there are no options to quickly revert to inherit or change all to revoke.
When creating usergroups or once created, there is no option to copy or base permissions on an existing usergroup or alternatively create permission templates as suggested before.
Ideally I would like to be able to be able to quickly change all the permissions of a usergroup in all the nodes, or be able to change multiple/all usergroup permissions of a node at once. I suggested a way to do this back in the vB days though I'm not sure yet how to make it XenForo elegant :/
I hope some of this suggestions will be taken up to make life of those of us with unreasonably large boards a bit easier to manage.