PCIe connected ssd's have a better bandwidth due to the PCIe connection and so have far higher sequential read/write speeds, while this looks great on marketing it makes little difference to most work cases over a SATA 3 connected SSD. Fusion drives are actually a software solution to organising the data on 2 drives a PCIe connected SSD and a normal hard drive in the iMacs, although this can be enabled on any 2 drives installed in a Mac even 2 ssd's.
Older generation ssd isn't fast enough to reach bandwidth limit of sata3 interface, so there wasn't a problem. When ssd becomes faster, a faster interface is needed. That's pcie. Normally pcie based ssd is faster on both reading and writing comparing to sata based ssd. Fusion drive is apple's hybrid drive. It is combination of a small ssd and a large hdd. Frequently accessed files are stored in ssd. ssd also serves as a writing buffer. A very small portion of ssd is used as buffer zone. File is written into buffer zone first, then transported to hdd in background so you won't notice the slow down. A very large file could use up that buffer zone, reducing writing speed to hdd level. Also, if you launch a rarely accessed file, it would be very slow.
I found my Fusion drive to be near SSD speeds. The boot up of OS X, is blazingly quick. My apps fire up with little to no bounce. I'm finding the Fusion drive to be fairly quick. I may not be testing the speed scientifically but compared to my MBP with a SSD, many of the tasks are just as fast.