Ripley's daughter isn't "crucial." Nobody was ever confused about her relationship with Newt for like 2 decades before the Quadrilogy made the Special Edition easily available. But it doesn't hurt the movie either. It's a nice little humanizing touch. It should stay in the movie.
The colony scene is terrible for tension-building. Ideally in horror films, the characters should encounter the "monster" at the same time as the audience. Even though it's a sequel, and the audience "knows" what happened, showing what happened to the colonists spoils any tension of the colony search. Cutting it out was the right idea for the Theatrical Cut. It's a fun worldbuilding addition for a second viewing. Same with the Ant Hive lines, which he also decides to cut.
Hudson's speech is fine, but it needs to have the audio fixed to remove him saying "Check it out" three times.
The gerbil/hamster scene should go. It is a "motion tracker fakeout" which is fine, but that fakeout happens twice in the movie which detracts from the tension of the second one. Since we need the Newt scene, this one needs to go. Not finding anything is way more scary than a cheap jump scare. The rest of the extended colony search footage should stay.
There's no "action" in the sentry guns scene. It's almost entirely static shots of faces, computer screens and sentry guns rotating. And it re-uses VFX shots of the Aliens dying. Very visually uninteresting and lacks any dynamics. It also makes the Aliens so stupid that they charge into 2000 rounds of machinegun fire. The sentry guns can stay in the film, but it should just be one scene (in the movie at the place with the second scene), and have the Aliens give up faster. Cut out the last shots of depleted ammo counters (so we don't know where the guns stop) and have the Aliens give up. You cut Hicks's line in the second scene of "next time they walk right up and knock" and go straight to Ripley's "They're probably looking for other ways to get in. That will take them a while." Fixes the problem with those scenes. Keeps the sentry guns (cool world building), keeps the Aliens dangerous and scary (as opposed to so stupid they charge at machineguns), and, like getting rid of the gerbil, reduces the redundancy and pacing problems of two scenes that are exactly the same and don't add anything to the story by having two of them.
