I think most FCP users experience the same problem with native 5d2 files (my guess is extra overhead in FCP or PP).
The best workaround is to import the files (at greatly increased file size) using the Apple Pro Res 422 intermediate codec (not the HQ version). This is lossless, will play and edit smoothly & give greater ability to colour correct etc. Edit, then export to your format of choice.
What do you recommend to do this? I have PremPro and FCP.