I hope the big meanie aliens have a really good reason to be antagonistic towards us newcomers and aren't just a generic war like ******* race. I'd like to see us do something more than just accidentally invade their space. Perhaps we settle down on a nursery planet that they terra formed for their young ones and we accidentally kill their babies as we don't recognize them as sentient life. Communication problems and cultural clashes, like you mentioned, just aggravate our horrible mistake. Something like this gives the aliens very good reason for going to war with us and paints the aliens in a more sympathetic light.
I agree, we shouldn't be presented with a native alien species that attacks us for the evilolz, and thus painting us "Milkies" as blameless white knights completely freeing the player of any and all repercussions as we proceed to shoot hundreds of them in the face. On the other hand, the narrative shouldn't go to the other extreme and paint the natives as this quasi-mystic people that can do no wrong while we, the evil invaders, slaughter them for their land.
As many like to point out, the parallel between this (supposed) premise of Andromeda, and the colonization of the Americas is very obvious, but BioWare's writers really need to take a balanced approach to constructing their narrative here. Because, as we had in real life, there were angles and devils on both sides of the colonization efforts, and trying to completely whitewash one side over the other is only going to do the story a major dis-service.
I'm glad I'm not the only person in the world who thought Avatar was Fern Gully with Smurfs...
(and a lot of "borrowing" from Roger Dean)
Avatar was Fern Gully/Smurfs/Dances with Wolves, and it managed to be one of the very few science fiction settings to actually make me like the humans over the aliens. Normally, I find us to be rather "bleh" in such settings, but in Avatar, the whole "We are a noble, and perfect people" trope of the Na'Vi was so obnoxious that I was wishing that the humans would have pulled an Alien and Nuked the entire site from orbit.