The FreeBSD installer currently only supports installing to bare drive partitions using UFS.
The PC-BSD installer supports UFS, ZFS, and I believe gmirror. There are plans to incorporate pretty much all of the GEOM options.
For installing FreeBSD, the end result (installed OS) is the same. How it gets installed, though, is different.
So, you have to ask yourself whether or not you need more than UFS on disk partitions. If you do, then use the PC-BSD installer.