Cant really decide between covenant & the flood, in the games they have been they work really well together.
Covenant is really the base of the enemies in Halo franchise with familiar species having balanced weapons opposing the human armaments with plasma working better on shields while bullets work better on hp.
The covenant used to be the one presenting more advanced technological threat which had great resources in disposal of let's say, fanatic leadership to keep this short.
Individually, even though usually physically more imposing than regular humans, covenant species became more like cannon fodder, thats where such things as scarabs came in the picture, a technological miniboss, depending obviously about which type of scarab is in question.
Still, covenant species have potential for display of quite a clash with lots of blue explosions meeting the reddish fires of human technology for example with space battles & why not even return something like the scarab? As in a type of miniboss that is not scripted to just walk past once & then on the next area just stick on one place while some nearly regular mob fight consists.
So, covenant still has some potential as enemies but the problem with them now is that they have lost much of their variety thanks to lessened importance of vehicles which in turn is thanks to some extra animations in mobility while on foot.
Halo really needs the covenant species as much as doom needs its demons, imps & other classic foes.
So then I could move onto the flood, now, as the covenant establishes a powerful technological foe, so does the flood represent a powerful biological foe, simply put. As what they bring to the gameplay is the agile, large in numbers natyrally & usually melee based enemy which also utilizes what it consumes, this gives flood some mixed weaponry, even on range which can make them deadly in numbers with bost plasma & ballistic type of weaponry.
The floods strenght in general doesnt come from their individual strengths but in their numbers, the mob enemies are just husks of the fallen accompanied by sluggish carriers & fragile infection forms. Most of those can be gunned down very easily but the thing is, they rise back up, and that means movement is survival & that destroying the flood means bringing in the big guns. This presents opportunities for cleansing missions.
Now flood has rarer cases of individual strenght or rather collective, physically collective infact. That obviously means the floods ability to assimilate bodies to form some imposing beings which could be used as boss material & this aspect of them has been pretty much overlooked though Halo is not specifically known for boss battles to be fair.
Then there is the minor horror aspect of them, every dead being means reinforcements or more mass and resources for the flood. The way this is accomplished is not very pleasant way indeed but it kind of adds as to why the flood is the only enemy the covenant fears.
So there we have the balance between the opponents in Halo, both factions with their own role and purpose.