- Isaac Clarke
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Solving problems you could have solved by yourself since 1968.
[i]- Veteran Stormtrooper Clarke of the Ordo Malleus[/i]
Life is too short to get irritated because someone's preferences differ from yours.
~ACP Cataclysm
It depends on what context you are talking about when you say the two fight. Are you talking about a 1v1 between similar lifeforms, or an all out war? I can't speak on the 1v1 very much (though I think that fresh necros would beat the flood), but I do have a lot on the war. Let the rant begin!
Basically, the flood infect other lifeforms by "hijacking" the spinal cord with the flood infection form acting as the new "head". No new nervous system parts are added. Destroying the original infection form stops the combat form in its tracks. Also, the flood is technically a parasite. More on this later.
Now then, the Necromorphs don't hijack a body, they take it, and create a decentralized nervous system. There is a lot of proof for this. To kill a necromorph, you shoot off its limbs. I could lose all the limbs on my body and still be alive. However, this completely kills the necromorph, not just disable it. Also, should you ever decapitate a necromorph, they start walking/jogging toward, wildly slinging their arms, trying to attack you (which is more dangerous than their usual attack methods). This implies that their senses are not exclusive to the head (like ours, I'm not counting touch).
The flood have access to all of their host's skills, the necromorphs do not. However, on the biological/micro scale, the necromorphs are much more adaptable. See: Wheezers. The Necromorphs find out that, surprise surprise, I breathe air. They poison the air in hydroponics, which is the part of the ship that all air circulates through as well as where new food is created. If this doesn't prove that necromorphs are more adept at adapting, then I'm not sure what does (other than the hunter or the convergence monster, which cannot be killed by destroying their limbs, as they just regrow them back).
Now, back onto the flood-necromorph war. The flood is a parasite by all means of the word. This fits the flood rather nicely. However, it is not quite clear what the necromorphs are, a virus or a bacteria (probably the latter, as viri can't reproduce to cover an entire hallway with organic much), however, it is clear that necromorphs can infect pretty much anything (or adapt to do it very quickly). Necromorphs would infect the parasite of the flood, and take over it with a decentralized nervous system.
Necromorphs would win the war, I'm afraid.
EDIT: Also, Flood can't use vents, and from what I've seen, combat forms generally aren't as flexible.
And another strategy that that the Necromorphs have is the fact that, while they can't operate machinery, they quickly destroy it outright.
Actually, on giving more thought, it depends on how advanced the technology used in the war is. If it's possible/feasible to glass a planet, have a space ship with shields, and nukes the size of a sun, then the Flood would win, considering the fact that Necromorphs cannot use technology (thankfully). Anything less than this "advanced space age" would result in necromorph victory. However, if the Flood only have access to Halo's human technology, I don't know who would win. It would depend on the Flood's strategy and number of ships.
[Edited on 01.31.2011 2:03 PM PST]