Qsys poor fmax peformance

Do you have a lot of fan in/out in your system? (i.e. a master connected to a lot of slaves or a slave connected to a lot of masters). If so you might want to change your topology a bit using bridges (and hierarchy).

Also are you constraining your design? If not then I wouldn't put too much faith in Fmax numbers even if it appears that the system works. I would look at the critical paths using Timequest to see where the longest paths are so that you know where to focus your efforts.