Under heavy I/O to the TDK branded 32 gig USB stick, the device lags pretty badly. Seems worse than just I/O performance on the USB stick, but I could be wrong.I think you're right. Booting in Linux, I see it to be snappier. When there's heavy I/O, it just becomes very very slow, much slower than expected. More, I've been also installing a complete NetBSD system on an external 5400rpm drive, and it's also VERY slow there.
I don't know about why a regular hard drive would be slower, but I know that WAPBL on flash devices seems not only slower but wears them out much more quickly due to writes in the same places over and over. I went through four 16 gig CF cards in a little more than a year before realizing and switching to softdep. Since then, I've been on the same card for more than a year now (same system, same brand of card, same uses, but softdep instead of WAPBL). It might be worth a try.