Think of it this way. Since the PCIe standard is backward compatible, the different components will use the least common denominator to operate together. So, stick a 3.0 device into a 2.0 slot and the device will operate at 2.0 speeds.
Insert a 2.0 device into 3.0 slot and the device will operate at 2.0 speeds.
Comparing the PCIe standards and their ability to work across versions (backward compatibility) may indeed not cause a bottleneck, but it is true that the devices will not operate to their full potential. In this example, something will have to operate at a level less than its fullest capability.
As mouse24 points out, it would not be a significant (if even noticed) degradation in performance for the VAST majority of users.