Well, I cannot really comment much on Samus, seeing I haven't rly played any of the games she's in... But saying Masterchief is just another generic FPS soldier that can't think for himself or run solo missions is a strange statement. I mean, most of the time you're alone. He decides to give the covenant back their bomb... when they're in space...and he has to fall about a km or 2 with an armed bomb to reach their ship and blow it to kingdom come.
He destroys the flood alone. He takes down all the prophets alone. He saves Cortana alone. He takes orders, yes, but that is because he is part of a military unit. But even though he is, he does things his way, and in the end, he will ignore all commands thrown at him if he does not think they're right.
I cannot say he is more badass than Samus, cause I don't know her, and thus cannot spwak on her behalf. But 117 is FAR more than just your average soldier who does not think for himself.
"He destroys the flood alone" No he doesn't. He had the Elites, UNSC, and Sentinels backing him up.
"He takes down all the prophets alone" Not true either. All through the level in Halo 2 where your chasing one done, the UNSC has check points where they send you backup and supplies. people constantly forget about the backup because on even on normal settings unless your a decent player they die rather quickly. At the end of the game where he's chasing the other prophets, he finds at least a DOZEN UNSC soldiers, not to mention the Covenant is busy fighting the Elites and the Flood at the same time.
On a "Badass" meter? chief's definitely beat her. Despite Samus' longer standing series and her iconic stature being the first female hero character, chief (and halo for that matter), is more popular. However, she's probably the more powerful of the two due to her armor and weapons being WTF OP by Halo Standards.