SirMaster,
I agree that the WebGUI does hide alot of stuff behind it. That *is* one of the drawbacks. However, it's also one of the strengths. I'd bet that 95% of FreeNAS users are flat out incapable of building a server with all of the features that they are using in the WebGUI every day. Why? Because the WebGUI has made so many decisions for you and has simplified things down to a point where many of us mere mortals wouldn't need to spend 6 months devoted to FreeBSD manuals just to be able to install FreeBSD, put a server on the domain, create a pool to admin (and actually admin it properly), and then share it out with Samba 4. That right there is a major undertaking for someone that may not have ever touched FreeBSD. Linux experience helps, but it doesn't give you the keys to the mansion.
In fact, about a year or so ago I was talking to a friend about FreeNAS (he loves zfs on linux) and some of those developers apparently feel that FreeNAS has made ZFS so accessible that it's actually depreciated the value of their product. They were wanting to be the ones to bring ZFS to "the masses" (small masses apparently) by making it possible to add ZFS to every linux machine everywhere. Instead they feel that people are moving to FreeNAS as a better, faster, easier alternative to getting a file server built quickly. I can't say I blame them. But, I do want to see ZFS on linux work because I do use linux and I do enjoy having ZFS on linux. I just wish there was a ZFS for Windows.