Here are some recipies to make ubuntu installed on USB drive to work faster.
reducing swapping
Add these lines to /etc/sysctl.conf, and reboot.
vm.swappiness = 0
vm.dirty_background_ratio = 20
vm.dirty_expire_centisecs = 0
vm.dirty_ratio = 80
vm.dirty_writeback_centisecs = 0
More caching while writting on disk
Add noatime,commit=120,… to /etc/fstab entries for / and /home