I would suspect that the fact that the installed system performs writes (which are inherently, significantly slower on flash media than reads), which the LiveUSB does not, will significantly impact performance.
I've setup an EeePC 701 to run from a 16GB SD card, and I did many things such as minimize logging (in my case, I disabled swap altogether, because there is no HDD to compensate, as you've done), adjusted mount options to include "noatime", to reduce writing updated access times to files...there are others I can't think of off the top of my head...I'd have to check.