1. I would say X parasites as long as there aren't any Metroids. But it seems that the Pirates always have some Metroids they've created from a little bit of DNA. So I could be wrong here and it could go either way.
2. I would say X parasites could take the Haloverse very easily, as conventional weapons don't destroy them. They might be able to destroy specific creatures that the X parasites have overtaken, but destroying the parasites themselves hasn't been possible without a Metroid or Samus.
I really don't think the Flood can handle the Metroid universe.
3. I will also say the X parasites. I'm not sure if you're allowing things like the SA-X or not, but if you are then I'm positive the X can win.
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All hail Scythe, King of the Sigs.
The X stomp the Flood into the ground. Had the X been able to get into space, they probably could have taken over Metroidverse. (I believe that Samus would have taken down the entire universe, but I'm just a fanboy.)
Yeah, the X would annihilate the Haloverse rather easily (Samus then takes it down, too) while Metroidverse wouldn't have too many problems with the Flood. And then all out brawl? X assimilate the Flood and improve them.