As per returning to the original subject 'the flood' We have never had any confirmation of the flood actually being entirely swept from the earth. As fleetmaster Rtas Vadumee said 'Once single flood spore could destroy a species' Although half Africa being glassed there is no certainty the flood was wiped out.
Now that would be some ending to Halo. Imagine, Master Chief fighting it's way of the Forerunner planet, escape on a Forerunner vessel only to find earth, humanity's last stand, been overrun by the flood.
btw, did the brutes not wearing armor really have a canonical reason? They had armor, only in small quantities. Bungie intended to make the Jiralhanae look like big, broad, loud almost uncontrollable beasts who stopped for nothing. Different sets of armor would have taken a lot of time to create, same with the lack of weapons and therefore seeing Brutes runnning around with rocket launchers and shotguns. Which canonical reasons were made up for -after- the games release. Now is it so hard to believe that it could have just been gamedevelopers rushing to reach a deadline?