We're only just migrating to Marketo, so I don't yet have any data I can draw on, but one thing I would suggest, though, is that you make sure that you're comparing like with like. Our previous marketing platform (Click Dimensions) calculated click rate in a very different way* to many other platforms (including Marketo), which meant our click rate was inflated. I am planning to be careful to 'translate' our historical data to make sure that I can get a meaningful picture of how performance compares under Marketo. This may not be what's causing your issue, but it might be worth eliminating that as a possibility.
James
* if a user clicks on two separate links in a single email, Click Dimensions counts this as two unique clicks, whereas for most other email marketing providers, click rate is the number of unique users who have clicked one or more links in an email.