Here are the basic differences between the cards:

1.WaveCenter/PCI uses the PCI bus, rather than ISA, resulting in faster transfers of audio data between the card and your computer's motherboard. In addition, the plug-and-play nature of the PCI bus makes installation a snap.
2.WaveCenter/PCI's MIDI configuration is 2x2, rather than the 1-input, 3-output configuration on WaveCenter-ISA.
3.All 10 of WaveCenter/PCI's digital audio inputs may be used simultaneously. With WaveCenter-ISA, only one input format (ADAT, S/PDIF coax, or S/PDIF optical) at a time is enabled.
4.WaveCenter/PCI includes MacOS support, in the form of an ASIO driver for digital audio, and an OMS driver for MIDI.