I'd have changed the interior look of the ship to start. It's so boring when the last act begins.
Skipping ahead to the juggernaut, I'd have them spot the city from the crash.
After the neomorphs emerge and start killing them like in the movie, I'd have a running battle through the dark to the city, like in the book.
I'd have them spend a short time observing engineer technology and architecture, just to finally give us something to see, including David's lab. Asking questions and staring in horror at a dead civilisation. Then I'd have them find David and shaws remains, Shaw having killed him in self defense with an axe, and then herself dying of starvation or the pathogen. Meanwhile, Oram snoops around and gets himself facehugged.
Then I'd Give them about 5 or 10 minutes to evacuate at night and in the storm with neomorphs in pursuit. Oram survives but is too confused and weak to understand what happened, or is hiding his condition and hoping he'll be fine. He bursts onboard the covenant. A biomechanical xenomorph. David had perfected his creation. The last 30+ minutes of the movie is slow death and horror in the dark, similar to the original. Lope would also still be alive, and acting like a security officer, not some cry baby leaving his men to die like in covenant.
The movie ends with everyone dead, and the alien hiding and going into hibernation. As the covenant sails on to origae 6, where the colonists will wake into hell.
Mid credits - a moan is heard in the dark, as we see daniels or others dying from egg morphing, the eggs to be used against the colonists.
