My biggest issue with A:C (and PROM) is the non-Alien movie structure. I'm not talking about the story structure etc., I'm talking about how the prequels aren't bound to the here-and-now real-time principle, i.e. I'm referring to flashbacks and the memories of certain characters. In the original Alien movies everything enveloped in front of our eyes and thus we, the audience, had to put the pieces together. I shrouded everything off the screen in mystery. We didn't get to see what caused the Derelict to crash, or get to see some emotional memory of Ripley and her daughter Amanda etc. Everything proceeded chronologically within a set time frame.
A:C (and PROM) on the other hand is peppered with these offshoots (especially referring to the extended cut), which makes it all feel less immersive and "real", but most of all less mysterious and enigmatic.
If I would have edited A:C I would have cut the intro scene with Weyland and David, and I would have cut the bombardment scene of the Engineer capital as well. The content of both scenes could have been told in a different way and with different story devices.
For example, the mausoleum of charred disfigured humanoid figures would've been much more eerie if we didn't get to see what happened to them. Did David really kill them all or did he land on a planet already devoid of organic (meat) life, except for the remnants of black goo organisms? If he didn't kill them, then how long ago did this holocaust happen to the engineers on the planet?
I have other gripes with A:C (for example the totally off-character scenes where the cast go all Rambo Hollywood movie - yes I'm talking about the ridiculously stupid flying barge/crane fight - the most idiotic Alien move action scene and sequence EVER - it's almost AVP:R stupid!).
