Heres where I personally dont really know an answer as to why the movie is disliked. Here are the most common arguments:
1. They killed Hicks and Newt
Thats a part of the story but doesnt make the movie a bad one. Sure, we bonded with the characters and didnt like the sight of them dying in a horrible crash, but thats part of the story and mood setter for this installment in the series. Plus, it presented a new challenge for Ripley, who lost everything twice by then and became completely drained.
2. Its too depressing
Again, it doesnt make a movie good or bad, it just a type of story. Depressing does not equal bad, nor does it equal good, its personal preference
3. faceless characters
I believe the characters that actually contribute to the story are fleshed out very well, which is a great accomplishment because theyre all bald and dressed the same way, yet its their personality that makes them distinctive. Morse, David, Golic, Dillon and on and on. The alien meat is faceless, but with so many prisoners why would we want everyone fleshed out?
4. magic egg
Lets not kid ourselves, the egg is there cause the movie needed an alien. As to how it got there or why in such position or where it was, look- its a movie, I know the first two took a great care in details but its no crime at all to take some cinematic liberties for storytelling purposes