With few exceptions, nobody has designed new PCI hardware in about six or seven years. Thus, any improvements in the technology usually won't show up in the PCI space. The few manufacturers that do are companies like MOTU that build breakout boxes that connect to both PCI and PCIe cards (since PCI is pretty much officially deprecated at this point in favor of PCIe). As a result, PCI (with the exceptions noted above) is starting to fall behind a bit in sound quality.
You're right, though, that PCI can get slightly better latency than FireWire or USB. PCI latency can get down to about 1.5 ms, while I think the record for FireWire is just shy of 2 ms. For USB, I think the record is just shy of 3 ms... if you're willing to burn that much CPU power.
The Lexicon Alpha is a fairly low end interface, so I'm not surprised you didn't care for the sound. If you want a big step up in quality, your best bet would probably be hardware from Echo, Apogee, MOTU, or RME. In the midrange, you might consider Edirol, M-Audio, or certain models of hardware by Presonus.
