Ive found that the halo universe and Starcraft 2 universe are quite similar. They both occur in the 26th century, and have 3 warring factions and a predecesor race (Forerunner and Xel-naga).
Ive found that the main difference between these two universes is the level of intensity of everything.
Take for example the difference between the Chief and an SC2 Marine:
A Marine is probably just a little weaker than the chief in terms of fighting strength, as they both have armor, weapons, and super strength. The thing is that the marine is the 2nd weakest unit in SC2 and can be produced in mass number (you better have Siege Tanks when you have 200 of these bad boys knocking on your door) And even though there are similarities in technology, like Hornets and Banshees (SC2 banshee, not Covenant), one thing that the Terran have are assault walkers like Thors and Vikings.
The Covanant's counterpart in SC2 is the protoss. They both are quite ritual, and have more of a smooth, energy based tech. However, somthing that is not wielded by the covanant is Psionic energy. The Protoss technology is largy based off of psionic technology, like their psi-blades and psi-storms (the bane of my Terran existance). However, even without psionic tech, their technology is still far greater because of things like their ability to warp in units strait to the battlefield and their robotic combat units (like Collosi). Despite these advantages, the Protoss are by far outnumbered by their enemies while the covanant are in mass numbers.
A fight between the Flood and Zerg would definatly be an interesting one. The flood bolster their ranks by reanimating and infesting the enemy units while the zerg devour everything in its path and use the resources to spawn and infest more units. In terms of unit strength, It would be close because, although the zerg can shred metal with their claws, the flood destructivly overclock their hosts body to achieve a similar level of strength. Of course the zerg is much more diverse in its possible unit combinations. The battle on the genetic level would be quite perplexing as well. The zerg mutates very rapidly, constantly throwing off new mutations. At the same time it is having a competition on the cellular level between the new and the old mutations, in which the stongest one survives. Because of this, the flood virus could infest the zerg, however it is possible that the zerg could mutate an immunity to it. The same is also possible that the flood could adapt to the zerg immunity as well. In that case, no real winner could be drawn because it would be a back and forth battle. They both are hive-minded races as they are all dictated by a controling entity. The Zerg is controlled via Psionic Energy by Kerrigan (It used to be controlled by the overmind, but it got killed) while the flood form a "GraveMind" from a critical mass of tissue.
I wont be comparing the differences between the Forerunners and Xel-naga because, number one this rant is getting too long, and number two, Xel-naga technology is too sparse for an accurate comparison.
With all things considered, I would have to say that the Starcraft universe would probably trump the Halo universe.
That, ladies and gentlmen, is the end of my crazy rant.
-Gryphon