Depends.
http://www.anandtech.com/storage/showdoc.aspx?i=3531&p=30
This illustrates it best I'd say.
On the one hand you have a game situation where lots of random reads made SSDs better, and therefore a flash drive might perform better than a regular harddrive, but in the second you have an example where there is little difference, and the poor transfer speeds of a flash drive would probably result in worse performance.
Basically in theory a USB flash drive wouldn't be terrible if it wasn't on current USB, which is pretty damned slow (30MB/s maybe). The only place where it could beat a regular harddrive is if the situation had a lot of random access, but even so the Flash drive might not be great because it probably wouldn't be optimised for doing that sort of thing, and it's not going to have the sort of controller an SSD does.
The only way to tell really would be to test it yourself, but I would be surprised if you saw any improvement at all, and most of the time it would probably perform worse.
One thing you could do is use junction points to spread the data so that some is on the flash drive and some on a regular harddrive, and that might work to improve performance in a few situations.