Back in the original Metroid games, we were shown that the Galactic Federation was a collection of races joined together joining together in peace. Then Metroid Fusion comes a long and reveals that much like the Space Pirates, the Galactic Federation was trying to breed Metroids as weapons.
You seem to be mixing your comics up.
video games always worked better without the grit of realistic politics thrown in. Then again the Prime series showed the federation experimenting with phazon based weapons (at least they didn't mutate the space marines with it...) and even idealistic shows like Star Trek had their share of corrupt government officials and politically motivated campaigns.