I think the reason why it was not well received was that, unlike its cinematic parents, AvP was rated PG-13. People went in expecting a glorious bloodbath with knockdown drag out fights and seeing humans dying in extremely violent and gory ways, but what we got was... sanitized. The violence and destruction seemed almost stylized instead of the visceral experiences we got from the predecessor films.
Don't get me wrong, I liked the movie, including the back story and all that jazz, but it seemed like when it came down to it, the film was lackluster and pulled that gut punch when it should have delivered it full force. Basically, it is the perfect example of what Deadpool would have been like if it was rated PG-13.
In contrast, the rated R sequel was the exact opposite. It pulled zero punches when it came to violence and gore, but the story was lacking severely. Plus, it was dark. Not atmospherically dark (even though it was), but just poorly lit. I hope the lighting guys got fired over that movie.
If we could have combined the best elements of the two films, it would have been a glorious film to watch.