There are various tweaks or features here and there I can think of that are missing from the GUI, but are supported in FreeBSD. Some of the things I can think of that I've seen or heard of on dedicated APs but are missing: association control by MAC address (whitelisting or blacklisting), WPS, WDS, and controlling the channel width (5 MHz, 10 MHz, 20 MHz - default on non-N, 40 MHz - default on N). These are already all available in FreeBSD, but no code has been written yet to take advantage of them from the GUI (except there may be a partial implementation of association control by MAC address that is currently disabled).
Also there is 802.11n, which is supported as far as running the card in that mode, but I don't know of any FreeBSD drivers that have working 802.11n rate control yet, so it is not yet possible to actually use the faster speeds in that mode.