I don't understand all the animosity over this either. The reason there was a Director's Cut to begin with was because in 1990 a workprint version was screened by mistake instead of the theatrical version which is basically a different movie all together. This "workprint" was supposed to be the theatrical version, but due to poor screenings, the studio decided to add a "happy ending" and add voice over narration, both over Ridley Scott and Harrison Ford's objections. The Final cut is essentially the Directors Cut but a much better transfer (the directors cut dvd looks like they used a VHS source for the transfer) and a few scenes tweaked here and there (wires digitally removed from the spinners, original actors filmed digitally to replace obvious stunt doubles, etc..).
I have the HD-DVD 5 disc set (the non-briefcase one) and it's amazing. It's a visual masterpiece, it almost seems like it could be released now it's so good. I recommend this for anyone interested in Sci-Fi or just cinema in general.