My cents, in terms of different cuts of the Alien films:
Alien (1979) - Theatrical cut, hands down. Even Ridley Scott prefers it.
Aliens (1986) - Theatrical cut is better paced but is missing crucial scene of Ripley finding out about her daughter. Special Edition severely suffers in pacing because it throws in material that Fox cut for time, as well as additional deleted scenes. The Fox TV cut, which has some but not all special edition material (thankfully omitting the shake-and-bake colony scene), likely resembles the cut that Cameron originally wanted to release in 1986.
This cut can be assembled by playing with the seamless branching on the BD. Also, I believe a preservation of it might be coming eventually.
Alien 3 (1992) - Assembly Cut almost feels like a different movie from the theatrical cut with far more character beats and an intriguing subplot. Ideally, however, the perfect cut would resemble the workprint more (no mysterious egg on the Sulaco, theatrical crash, no basement scene, etc.).
Alien: Resurrection (1997) - Theatrical cut wins again. Special Edition is just an oddity created by the studio.
Prometheus (2012) - The theatrical cut is so deeply flawed that I prefer to watch fan edits of this one. Prometheus Unbound is the best iteration I’ve found of all the ones available, wonderfully tight with the characters of Vickers coming across as far less 2D. For a “Special Edition,” which throws in all available material, I would recommend Agent9’s Prometheus: Special Edition.
— SPOILERS FOR FILM CURRENTLY IN THEATER —
In terms of Alien Covenant, I figure an ideal cut would just remove the 3rd act Alien throwback stuff on the spaceship near the finale, and better edit the Walter/David fight so the “twist” wasn’t so obvious. Hopefully, there’ll be deleted footage to play with here.