You'll find that almost all of the default HTC applications stayed in /system, as well as most of the Sprint applications (the ones that weren't removed anyway). The logic behind this, I believe, being that these apps aren't available on the market so there's no need for them to be in a read/write partition. The apps that did get moved out have market versions, and were moved to make them easier to update.
Also, since they're stored in /system which is all OS and other static files, you don't gain anything by moving them out. You don't get to use that space under normal circumstances, so there's no reason to 'free it up'