Generally, a virtual SCSI drive will perform noticeably better than virtual IDE. Because of that, a virtual machine is set up with SCSI whenever possible (the exceptions being XP outside Easy Install, because XP doesn't ship compatible SCSI drivers in the box, and the Boot Camp partition, which talks directly to the physical SATA drive in your Mac).
But I don't see how awake-after-suspend would affect things. Might you be constrained on RAM, in that other things on your Mac use up the physical memory while the VM is suspended, and it takes time to rebalance the working sets? If you've paged everything out, it will take time as memory and Fusion code comes back in at the same time the VM is trying to access the virtual disks.
Does it get better after two or three minutes of use?