As one who has used both the FA and DFA 50mm f/2.8 Macros and the FA and DFA 100mm f/2.8 Macros, there are noticeable differences between two series. First off all are usable on 35mm film and digital (i.e. FF compatible) with an image circle larger than APS-C.
The first thing that is immediately apparent is that the DFA macro lenses have been made more compact and lighter in weight compared to the FA macros. There is plenty of polycarbonate plastic in the construction of the lens barrels. The lens barrels extend outward necessitating the use of the large plastic lens hoods both to shield from glare and to protect the extended lens barrel. The FA macros are more solid in build quality overall. One aspect of the slimming down is that the DFA lenses use the same 49mm filters while the FA 50mm and 100mm macros use 52mm and 58mm filer sizes respectively. No hoods on the FA macros as the front element is recessed.
The smc PENTAX-DFA Macro 100mm F2.8 incorporates the FREE (Fixed Rear Element Extension) focusing system, while the smc PENTAX-DFA Macro 50mm F2.8 features the dependable floating element system. These reduce aberrations at any focusing distance to infinity, a bug bear of older macro lenses which are typically sharper only at macro focusing ranges. No issues with the FA macros in this regard.
Since much of macro shooting requires precise focusing, the DFA's wide focusing barrel and Quick Shift is in practice much better when focusing manually than the FA, which requires disengaging the AF before manual focus can be attempted. With the DFA, one could get the camera to AF first before being overridden with Quick Shift. Due to the long focus travel, both DFA and FA macros can hunt if there is no subject or adequate contrast to lock focus. In this regard, the DFA is a little better, but not by much.
If I had to choose, I still prefer the FA macros over the DFA macros when it come down to optical performance, but only just. The DFA versions have a much snappier, brighter overall contrast, typical of DA lenses whereas the FA version give a much nicer, punchy colour rendition. In extreme high contrast situations like backlighting, there is some colour fringing and highlight blooming at larger apertures for the DFA. In terms of sharpness, there is little to choose as they are all very sharp and aberration free, but the DFA will give the appearance of being a tad sharper due to the higher contrast. On balance, you can't go wrong with either version, though if you shoot for an extended period, the lighter weight of the DFA versions is noticeable and less taxing, particularly the 100mm. If you can look beyond the plastic build quality, the DFA is not a bad option, particularly with the very useful Quick Shift.
PENTAX Press release 2004