Real advantage? No. The difference between 3 milliseconds (PCI/PCIe) and 6 milliseconds (FireWire) of round-trip latency is inaudible. There are, however, advantages of either FireWire or PCI over USB in terms of reliability.
In general, I would suggest avoiding PCI-based interfaces. Legacy parallel PCI is being phased out in factor of PCI Express (PCIe). As such, interfaces that require parallel PCI are not a very good long-term investment.
There is one exception, though. Some outboard interfaces are available with either PCI or PCIe cards (e.g. the MOTU 2408 that works with either a 424/424X or 424e card). For interfaces where such alternative main boards are readily available, those are a decent choice. I would generally suggest getting the PCIe version, though, unless you're buying used.