In Halo most things have an at least psuedo-scientific explanation. Shields are a kind of force field. Covenant weapons fire superheated plasma with magnetic containment. Spartans are humans with DNA enhancements and in some cases extreme rebuilds of their body...
And the flood are telepathic matter-generating magic beings that can remember things from the past?
I'm using this site for most of my information: http://halo.wikia.com/wiki/Halo_Nation
First the galactic strategy of the flood. They are reliant on consuming hosts for biomass. They do have the ability to create pure-forms but these are a last resort, rather than a primary means of procreation. So why does the mission statement of the Flood say "consume all life in this Galaxy, move on to the next"? Even the most basic of strategies would be to keep a portion of the populace alive in captivity and have them breed to ensure a good rate of growth and capability to fight a potential enemy that doesnt leave hosts, like the Prometheans? But for some reason the Flood doesnt do that and happily consumes all life in the Galaxy until nothing is left... While their demise came from the Halo Rings which destroyed all life they could feed on...
Then, the flood are all telepaths. Or actually the Gravemind is, and it can control all floodforms with FTL commands. Before a Gravemind they use pheromones. So why can't the Gravemind just control living beings? The Gravemind at some point is able to talk directly to Master Chief. Yet this ability isnt used anywhere else?
The flood also creates matter. Creating a Spartan super-soldier requires top physical subjects with extensive rebuilding and DNA changes so that Bob the basic-training soldier can hardly kill Master Chief when he's sleeping. But if the second lowest but extremely numerous floodform gets a hold of Bob's plasma-burned dead body for a few minutes (current lore) or hours to days (old lore) it can rebuild Bob's burned corpse into something capable of beating an armored and shielded Spartan to death. Just thrle rebuilding into a living being requires generating energy-rich material out of nothing, and even then it should be taking weeks not days or minutes.
And ofcourse the Gravemind is capable of remembering knowledge of the previous Gravemind. It's alluded that the Flood can store knowledge in lowet floodforms despite the fact that after the Hosts knowledge is taken the mind is destroyed as a precaution against influence of the old host. This is a nice safety measure should the Gravemind be killed. But after the Halo Rings fired the Flood died out and the flood still kept for study would be too few in number to store the immense amount of knowledge the previous Gravemind imparted.
Then there's the spores. These airborne flood viruses are supposed to mutate anyone who breaths it and theres effectively no cure... But we have Elites, the Arbiter in particular, that have been in flood infestations without breathing protection. The Arbiter is also seen losing his shield in a cutscene in the middle of a flood infested area, so his shield can't have protected him and after the events of Halo 3 a large flood infestation should have engulfed the Elite worlds as infected Elites turn.
So why are the Flood this mess of "oh noes unstoppable virus with ultra-intelligence that consumes all!" but when it comes down to it the Flood's most basic principles of operation are dumb as a brick and they aren't as unstoppable a virus?