So what happens when the PCIe bus is updated and/or replaced in the future with something better? Can Thunderclap adapt to future bus changes or will it then become obsolete (i.e. being the PCIe bus in its current form)?
If the motherboard abandons PCIe, then the mobo controller for ThunderPort would need to change. It could still output PCIe signals on the cable and map them to the new mobo interface.
Busses tend to change slowly, and overlap for many years. Many motherboards still have PCI slots for older cards.
If ThunderBolt can mix DisplayPort and PCIe signals on one set of wires, a higher bandwidth version could even multiplex a third protocol on the wires, so that the new native bus could be used in peripherals.
One thing that I wouldn't expect to see is for TB to become as cheap and ubiquitous as USB. There are too many costs embedded in the chain.