i have to agree with The Jackel, the way i took it from the start was that the marines were there first therefore Samus was under their jurisdiction... you see this all the time in the entertainment media, like in cop shows, where a P.I. walks into a crime scene and the local cops tell them you have to play by our rules, it's a common plot device and i don't see why people are getting worked up about it...

i've been playing the Metroid series since it first came out on NES, i have every installment (except Metroid2 for GameBoy since i didn't have one as a kid, but i played it on my cousins GB), and i have to say i'm very pleased with the direction the series is taking in showing more of Samus' character as it was portrayed in the manga, honestly i feel it fleshes the character more...