Lance Henriksen has some shockingly direct comments that play during the closing credits to Alien3 on the commentary track. He basically says, "I'm not sure who the audience is supposed to root for in this film. The murderers and rapists don't really earn, or deserve it." That does seem, to me, to be the major flaw.

Aliens, in 3 Acts

Let me give this a shot. I think you're right, there is some stuff before the real story starts, but lets call that a prologue and not act 1.

Prologue- Ripley is rescued and goes back to Earth.
Act 1 - Ripley joins the Marines' mission, all characters are introduced, and Marines land on LV-426 and find Newt. THE PROBLEM: Aliens have taken out the colony.
Act 2 - The Marines find the hive with the colonists, the aliens attack and kill half of the force. The rescue/kill the alien mission is scrubbed and they decide to tactfully retreat. The aliens attack the drop ship and it crashes. They decide to set up the antenna to remote pilot the other drop ship planetside. THE PROBLEM GETS WORSE: The Marines can't just shoot the all of aliens. There are too many of them, and they are unprepared for the assault. They lose half of their team and decide to retreat.
Act 3 - This begins when Newt is taken by the aliens and Ripley decides to rescue her. Against unsurmountable odds, Bishop is able to bring the shuttle down, and Hicks, Bishop, Ripley and Newt escape the planet.
Epilogue - The Queen is on board the spaceship. Ripley kills the Queen once and for all, and they all go into stasis for the journey home.

Please submit your disagreements.