Currently only the Missions folder supports subfolders, which are a great help as we can make subfolders for cwr2, ACE, Vanilla etc and then when we launch with certain mods, we can easily identify which missions are compatible with those mods and can be played. It also makes it far easier to manage the folder and the files in it with Windows Explorer
The MPMissions folder needs to support subfolders as well, as currently if we create subfolders and put missions in those, ArmA can't see them and having everything in the root makes it a nightmare to manage in Windows Explorer.
The MP Create Game screen currently filters missions by island, which makes it very difficult to locate a particular mission and is not user-friendly. It should support subfolders so that where it currently lists islands under Map, it would show any subfolders, with the missions in the current folder listed on the right in the current Mission area. However, this list should group the missions in the current folder by island in alphabetical order, so for example at the top it would show a header Bystrica with associated islands underneath, then a Bukovina header with associated islands underneath, etc. This method would accommodate those who for whatever reason prefer not to use subfolders and have all MPMissions in the root folder and still allow them to choose a mission by island, as well as those who want to use subfolders to group missions by whatever categories (mods, islands, etc).
For Campaigns, it might not matter so much, particularly if Automatic Mod Enabling is implemented as requested here http://feedback.arma3.com/view.php?id=6428#bugnotes but it can still be useful to quickly identify, both in-game and in Windows Explorer, which missions are Vanilla, which only require mods such as ACE or CWR2 and which require a variety of mods, so I would request subfolder support for Campaigns as well.