Since I believe this suggestion is likely too radical I'll likely unsubscribe to most, if not all, of my user folders placing the special folders at the top of the list. I'll then have to subscribe to a user folder if needed.
Let me ask you: Are you actually receiving any incoming mail to the "subscribed" folders? (I.e. do you have server-side filters that sort incoming mail into separate folders, and those folders are the ones that you are syncing in Aquamail?)
If not, - selecting those folder to sync on a regular basis puts an extra toll on your sync process (traffic and battery consumption). I don't know how big that is (it also depends on the number of folders), but it is non-zero.
The alternative to that would be to just open those folders "on demand", via "Other folders". Note that in that case these folders will stay in the menu for some time (configurable). By default, it is set to1 week, but you can set it to 1 or 2 months . Those folders are actually
at the bottom of the list. So, if you are accessing them more frequently then 1 or 2 months, - they will always be on your list. (And if you are not, - you don't need them.) Just increase the "Recent folder count" from the default "3" to how many you'd need, up to 50.)
Both options are under Settings -> Account list -> the last two options.
I think this should achieve what you need.
As an aside, - long time ago, in pre- pre-MobiSystems era, I proposed to Kostya to have a category of folders that are "pinned" but not synced. This would be useful for people who frequently "file away" messages from Inbox to several most frequently used folders, but don't need those folders to be synced regularly.
It even sounded he might think about that, but I understand that it was not a high priority.