Oh don't go there yet you two....
Throughout the Prime series there have always been big battles in certain rooms or areas, this one trailer doesn't mean constant fighting. The "Bridge Battle" there was part of a boss fight so its not like that is going to happen in every room or anything, aside from that the devs have been saying they wanted to give players a sense that while samus isn't alone in the universe (like it felt before) she is alone on her missions. Some of the content is supposed to have outside interaction, but for the most part we should still be getting the same Metroid Prime feel we love.
Edit: Just wanted to point out that you don't spend all your time on one planet this time, so its entirely possible that the first planet (the Federation Planet) has friendlies, while the rest do not...since it is a federation planet it makes sense for them to be there. They aren't just going to remove them if it makes no logical sense.








