I prefer the AC as well. The only thing I don't like is the alien being captured, but the positives outweigh the negatives in that cut IMO.
I didn't hate A3 the first time I saw it, I just thought it was a bit boring. But that changed as time passed and my taste evolved. As an ending to the trilogy, I love the thematic payoff. The polar opposites of standard trilogies where the entries have a optimistic-pessimistic-even more optimistic tone, whereas the Alien trilogy goes pessimistic-optimistic-deeply pessimistic. Love the subversion. That doesn't mean A3 has no flaws though... Of course, I only mean those perspectives in the broadest, vague sense of the word, implying the feel of the general movie atmosphere.
Damn it, I'm due for a rewatch of the original trilogy.