In fact, if you want to force your database to compact all the way down to just a single change file representing the reference database, you can go into Sync Preferences on the Mac, click the Show Clients button, and unregister every single thing on the list (including the local machine)—then Close the clients list and click on Sync Now. Just remember that unregistering a client will break synchronization with it
Does that help?
Now I have 1 glorious change file and even resetting the database (all I've tried so far) went from 2+ minutes to about 10 seconds.
FYI: I have a home computer, work computer and iPhone, at least one of which has typically not been synched for many days. So I clearly wasn't following your well-publicized best practices (which I consider reasonable given that I'm not aware of another app handling more complexity in less time than you guys).
ObligWhine: for the desktop app - can folders please, please, PLEASE behave (at least mostly) as a single-action list?
Having to create a "default" single action list call "Miscellaneous <folder_name>" under each of my 5-6 major folders is a PITA. I'd find it handy for two reasons:
1. I can't think of a time when a folder has had more than one single action list. But I nearly always eventually create a "Miscellaneous" SAL for each, which looks stupid.
2. As a folder-specific inbox. There are tons of times where I've had actions that clearly belonged in my "Library/Work/<Area of Responsibility (no, not Project) XYZ>" OmniFocus folder – e.g. I'm a product manager who owns two products, w/ a folder for each – but didn't have time to think about which of folder's several projects it belonged to, or whether they belonged to a new project. Leaving them in the master Inbox though adds noise there, that I'd rather keep to an absolute minimum. CC's Things allows you to park individual action items in Area of Responsibility, which I really like. That basically addresses #1.