Well, an integrated flash reader would probably run off SATA or IDE if you're unlucky, but both of these standards would still be slower than PCIe. I'm not sure by exactly how much, or if flash memory can fully saturate SATA. I'm sure that IDE or USB would be a bottleneck on the performance of a flash drive. I can't tell you whether 1gig in PCIe would be more beneficial than 2gigs in USB; I haven't tried either. Read the developer's FAQ
here for a few pointers. (SD card readers are not supported, apparently)
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P5N32-E SLI 8800GT Q6600
2gigs Mushkin Redline @DDR2 800, 4-4-4-10