You know it rather bothered me how freely you were allowed to come and go on the Citadel in a Cerberus ship. Omega and Illium sure, but the Citadel? The Normandy should have been impounded as soon as it cleared the mass relay. For that matter, even being able to visit the Sol System feels a bit odd as one would assume you have to pass through Arcturus first, and that system must be a fortress.
The Mass Effect Universe doesn't seem to be a military state, even the so called Dreadnought appeared to simply take licks, it didn't do anything in the attack. The universe isn't perfect but it serves the story just like everything does.