The single biggest thing that folks can do to speed up their syncs is make sure that all of their devices are syncing regularly - like once a week or so.
On one of your Macs, open up OmniFocus's sync preferences and press the "Show Clients" button. OmniFocus has kept all the individual changes you've made to your database since the oldest date you see in the "Latest Sync" column.
If that's very far in the past, you've likely got hundreds of transaction files built up, which can slow things down, especially on the phone. (The iPhone is an amazing device, but it's still about 1/2000th as fast as a slow desktop machine.)
In any case, if you unregister any machines you're not actually syncing any more, then make sure the remaining devices have all synced, you should start seeing faster syncs about an hour later. (For technical reasons, we keep the transactions around for an hour, then compact during a subsequent sync.)
If none of that helps, contact the support ninjas
and we can help out. (We need to gather some info that generally doesn't fit into a forum post.)