In this case, the power of the system is in its infinite configurability. I would venture to say there is really no "right" or "wrong" way to use pfSense.
There is also no way for pfSense to know what your real intent is, especially when it comes to configuring packages (which is mainly what you're talking about, squid, squidguard, etc). I don't know about you, but to me what you're suggesting sounds a lot like "Clippy" of Microsoft Office infamy. It shouldn't really be pfSense's place to second guess what an administrator is trying to do, since that is really up to the administrator.
The kinds of things you discuss are, as you hint at, things for the manual or book. There is a book in the works, and there is a lot of documentation on the Doc Wiki. Alternate scenarios and suggestions for better ways to accomplish a given task are wonderful to have there. That said, I wouldn't want them in the WebGUI trying to alter my behavior.