The Theatrical Cut is superior and is the definitive version of this movie
I consider all the Special Edition's additions of little to no value, and here is why:
Ripley's daughter - The goal of this scene is to establish Newt as the new daughter for Ripley. The first movie did not mention Ripley's daughter once, so this is kind of a neutral addition. We don't really need an explanation on why Ripley would try to protect Newt, any sane adult would do the same. Watching the SE, no one ever said "oh, so that's why!" - this does not add anything to Ripley's character. It was a good decision not to have it in the TC.
Hadley's Hope scenes - We don't really need them. I would even say that these scenes are harmful to the overall experience. It's much better to only see the colony in the aftermath of the alien infestation. Seeing HH operating normally cheapens the impact of the tour of the marines later in the movie - as we have already seen this place, and the buildup is ruined.
Newt's family expedition - This scene has no surprises, since the second they go to the derelict, we know what is going to happen. And it destroys the revelation which comes later, that Burke was the one that sent them there. The way it is built up in the TC is genius - we don't really think about "why now" until Ripley says that she looked up the orders and Burke sent them there. Not that shocking, but the revelation scene is full of raw emotion, impactful and effective. But it loses much of its effect in the SE - the audience just goes "yeah, I know that they were sent there".
Hudson's bragging - Bill Paxton is great, but this scene is just too on the nose. Even without this, the hubris of the marines is evident and well established during the movie. At best, it's a neutral scene, I don't miss it at all.
Hinting at the queen - Maybe the most iconic single shot in this movie is the queen revelation - and the impact is ruined if a queen is mentioned in the dialogue beforehand... The TC was right to omit this.
Ripley and Newt extra dialogue - This scene tries to payoff the buildup of the daughter scene, but it's really not needed to understand the character dynamic between them. Oh, and this:
When Ripley tucks Newt into bed, Newt asks about her family and if human babies come the same way as Chestbursters. Ripley, of course, says that it's very different.
This... this is downright silly...
The sentry guns - The sentry scenes cheapen the threat, as the aliens keep on swarming the chokepoints, mindlessly for a while. In the TC, they seem like much more sophisticated, as their first course of action is to come from the ceiling. So I don't mind it's not in the TC.
Ripley and Hicks first name exchange - This is kind of meant as a romantic moment between them, but we completely understand their relationship with the scenes given in the TC - so this is not needed.
Ultimately, the TC is superior for me, mainly because how perfect the buildup until the point we witness the hive. The fact that the marines are late to the party, and that we did not see the normal operation of HH beforehand, creates a unique atmosphere where it's up to the viewer's imagination to piece together what exactly went down. All the HH and the Newt family expedition scenes only cheapen this impact, which is counter-productive.
As I have shown, the rest of the extra scenes also don't add virtually any value. My conclusion: the TC is the best version of the movie.
Feel free to agree or disagree and add your thoughts.