Comparison images would be good, and to get the best overall quality for a slow-mo sequence you should really be conforming the footage. Here is a good explanation as to why you would want to do this: http://gopro.com/support/final-cut-pro-tips/ I think there is an adobe app in the CS suite that should do the same. Also, not knowing what the exact compression settings are don't help. Are you exporting using QuickTime or something else. If it is something else, it is going to be difficult to suggest settings to improve the quality. Also is it image quality that is degrading or is the motion off?
Many thanks for your reply. Someone on the adobe forum helped me out. In premiere I can choose a sequence by selecting the video and it will take all the settings of the video to the sequence. I have done that. I still the find the exported file a bit less in quality. I mean the image quality and not the motion. I have exported in H.264 - High quality - 720p - 59,97 fps - VBR pass 2 - maximum render quality and a bitrate of 6 and max 10. For a 12 minute video the file size was 550 mb.
The 60 fps mode of the camera (contour HD, almost same as GoPro) is really cool especially when you play in slow motion it looks really nice. I still think (not because of Premiere but also the raw shots) when you look at a 60 fps video it looks like it is in fast motion. Don't know why this is.