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We had the same issue at one of my past companies. What I would suggest is you perform an audit on the fields syncing over to Marketo from SFDC. Support can help identify the fields that are syncing the most data. We had tons of SFDC fields that changed frequently (and therefore were hogging up space in the sync queue) and were vital to our enigneers, but had no impact on our marketing programs. If you are selective on which fields are being synced to Marketo, you can greatly improve performance and clear some space in the sync queue.
Also, it would be awesome if we could see the sync queue, but it is not possible currently. I believe there is a community idea out there requesting this feature.