I know there was many enhancements to FFS in 3.1.4, being a long time PFS user I was curious if anyone had any comparison or thoughts favoring one over the other.
FFS structures carry a lot of legacy around, and if you would design a file system from scratch these days, there are multiple things you would probably do differently. But it's too late for that, FFS exists, and you cannot run an Amiga without it - so whatever you think about it, there is a need to maintain it and update it.
Actually, FFS has a lot of overhead when listing directories, but it has quite a low overhead when reading and writing files. Thus, for data-intensive (ehem, cough cough, Amiga...) processing, the FFS is actually quite good and well-performing, because its structures are simple and the data is just linear on the disk most times, allowing quick access to it. For anything else... well, you know it. Directory listing is slow, robustness is bad as there is no journaling... old stuff.
On the plus side, there are many tools around it, disk editors, disk analyzing toolkits, and -tada- a new disk doctor.
I assume legacy disk programs like Amiback tools do not work with the new FFS?
I do not know. It depends on what the program attempts to do. As long as it goes through the operating system, there are no surprises. Just that file names can be longer, but do not have to be longer. The interface did not change, so things should just work transparently. If the tool accesses disk structures directly, then you cannot use DOS\7 and DOS\6, the long file name mode.
You can probably use DOS\8, the "inofficial, I haven't told you, but still bugfixed and maintained" version of the FFS which has file names up to 52 characters long and whose structures are much closer to that of the regular FFS.