The whole thing with Ripley's dead daughter and having that be the connection she has to Newt. It takes away from what the sequel was initially about; Ripley healing from the trauma she suffered in the first movie. And doing so by helping a child who has suffered through the same. That was their connection, not Ripley having lost a daughter and Newt having lost her parents. We don't even know about Ripley's daughter till we hear she died, so why should we care? We don't know Ripley as a mother, we know her as the person who survived the Alien encounter from the first movie. That is our emotional connection to her.
Then there's the really, really bad scene that shows it's Newt's parents conveniently being the ones who got sent to the derelict ship, along with Newt. We also get to see the colony before the attack, which takes away the mystery and cuts the audience off from the perspective of Ripley and the marines who are going in blind. In the theatrical version we go in as blind as them and it adds to the tension.
There's the turrent scene which might have some effect if you've never seen the theatrical version, but if you have it has zero tension because you know the aliens don't make it in until later.
Also, having a slow pan through the Sulaco at the start of the movie feels like pointless padding. I know it's supposed to reference the first movie, but unlike that movie we barely spend any time on the Sulaco after we're introduced to the marines, and none of the tension takes place there until the very end. The first movie takes its time to let the audience familiarize themselves a bit with the Nostromo where most of the movie will take place, as well as its claustrophobic atmosthere, before introducing us to the characters. There is no need for that in Aliens and the theatrical version appropriately just cuts straight to the freezers as the marines wake up.