I don't know whether I'm too dumb or not dumb enough to grasp all the intricacies of CDC but, if I understand it, there are virtual serial port drivers for interfacing on the PC side. When these are used, there's likely to be a slight speed hit as the data needs to be 'translated' from its RS232-ish form before transmitting and the reverse is true when receiving.
This may not be noticed for normal communications but can be readily apparent when doing something like a firmware download which usuall includes short bits of data and CRC which is ACKed or NAKed from the embedded device. Of course, the faster the version of USB, the less this is a big factor.
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