There are several performance issues with using USB Flash as your main storage.
First off, USB2 is slower than SATA or even PATA. PATA tops out at about 133MB/s IIRC, though possibly 150 or 167. USB2 tops out at about 50 or 60 MB/s, and you rarely even see that in practice.
Second, writes to Flash are significantly slower than reads.
Third, USB flash isn't the same as SSDs. It's designed to be cheap, convenient, and portable. SSDs have very sophisticated controllers doing clever things to make things fast - you shouldn't expect that with USB flash or SD cards. And you should expect the problems to include long latencies (how long it takes to get started) as well as slow sustained transfers (how much happens per second once things are in motion).
One option that may be worth a little research is using a CompactFlash to PATA adapter.
The interface used for CompactFlash is actually heavily based on the interface for PATA. It's so similar that some people in the past have found ways to connect CompactFlash cards to PATA interfaces rather than use a hard disk - IIRC, it was a trick used by some retro computing fanatics at one time. There were certainly some adaptors you could buy, though as far as I know they were produced on a small scale.
I don't know if the CompactFlash-to-PATA thing will support the full PATA speed and DMA, but it might be worth checking. This has been a niche thing for a while, e.g. for retro computing or apparently as a replacement for 1.8 inch HDs in ThinkPads.
Even if the adapter allows full speed, though, the flash card almost certainly won't.