First off, the Guardian sites: they show up on the FSS scan, but not in the place you'd look. Rather, they are "hidden" (though still highlighted in yellow) in the optional "Locations" part of the text, and not the top right corner where Geological and Biological signals are listed.
The POIs themselves also appear if you are within 1,000 ls, or if you happen to point your ship at the body they are on.
Moving back to the FSS:
I'll refrain from saying anything about the shortcomings of the interface and minigame itself, and just focus on what went away when it was forced on everyone.
In a nutshell, the main issue was that it hid information that was previously immediately visible, behind a simple and monotonous minigame. (Which was designed as a time sink, and also to shower people with credits and tags.) If you were looking for interesting orbital configurations, or unusual surface features large enough to be visible from a distance, or green gas giants, or possibly other stuff I forgot, then once the FSS was added, you had to grind out the minigame to completion, just looking at the barcode wasn't enough. Only to find out that 99% (or worse) of the time, what you were looking for wasn't there.
To quote the developers (from a stream): "The key thing here, and in this bar, yes overall you're right, the [FSS graph] system is learnable, but what, what we're jokingly trying to kind of get across is that very quickly you can jump into a system, perform the pulse scan, look at that bar and say "there's nothing there that I want", there's no Earth-likes, there's no whatever you're looking for, and get back out again."
As you know, thin atmospheric bodies aren't visible on the bar either. So, if you want those, or any of what I mentioned above, it's grind time for you, and chances are you won't find what you're looking for, so it was mostly a waste of time.
You know, just this month, David Braben commented (on Twitter) on a GEC entry that I discovered: see
here. Now, luckily I found that one before the FSS, because after it, I never would have noticed the place. After all, this was how it looked upon entering the system:
View attachment 382364
But after the FSS, you see this:
View attachment 382363
So yeah, I would have missed it, and so would have many others.