Yeah, extended versions aren't necessarily for the better. I love the stuff in 'Aliens' which deals with the colony (it reinforces how dead it feeels by comparison, later on, when you see the residents and children going about their usual daily lives), but think it feels too coincidental to have Newt be a random last survivor and for her parents to be the ones which first encounter the creatures.
Then there are unexplained changes, like how the new version of 'Alien' reinserts the Space Jockey signal, yet changed it from genuinely unsettling audio to a generic digital signal, which makes the crew's reactions to it nonsensical.