We've had the same issues where syncs were waiting 3-4 hours or even longer; when the standard sync behavior is supposed to be roughly every five minutes after the last sync (with SFDC). We are currently using SFDC Performance edition that does not have any API issues. I opened a case and it was escalated to tier 2 and was investigated.
Eventually the case was closed and the issue addressed as such:
After a review of the sync process our engineers have implemented some improvements on throughput that will help to clear up bandwidth during the sync. You should notice the improvements over the next week.
I get the sense that there are some bandwidth issues in Marketo's infrastructure.
If you need more help I can provide you our case number if you want to chase it.