- Each has three dominant races
A lot of RTS games do.
- The three races are fighting conquest-style, though for Halo, they're rings, and SC, it's planets
When three civilizations fight to the death, how else will they fight? Besides, the Halo installations aren't the only things they're fighting for. See: Harvest, Reach, Earth.
- There is a human race, a technologically-advanced alien race, and an evolving alien bug race.
Three sci-fi archetypes. They could be practically anywhere.
- The human races both consist primarily of "marines".
There's a difference between the Terran Marines and the UNSC Marines. The Terran Marines consist of rehabilitated criminals (at least, that was the method used by the Confederacy). The UNSC Marines consist of flash clones.
- The advanced alien races both consist of a plasma-shooting, shield-bearing soldiers, usually fueled by some prophecy or belief.
Protoss use Phase Disruptor weaponry. They are the archetypical warrior-race in the sci-fi genre. The Covenant are a religious conglomerate of several different races.
- The evolving alien race is a mutation of other DNA thrown into their pool. The zerg units, are based off of other animal DNA from the series, morphed into the zerg unit base. For Halo, well, it's pretty obvious a lot of the enemies are mutated marines and elites.
The Flood are parasitic. The Zerg, in a way, are somewhat parasitic as well, but the Overmind is seeking to infest those with great psionic potential/power while the Gravemind simply wishes to consume all as food.
- The Protoss have a civil war. And in Halo, there is sort of civil war, between the Covenant and the Brutes, but it depends on your perspective if the two were even part of the same race (looking at all of them, none of them really seem like the same race anyway, apperance-wise).
A. The Aeon of Strife was years before the events of Starcraft. The Covenant Civil War was during the Human-Covenant War, and it was the Elites that separated, not the Brutes.
B. None of them are the same race. The Grunts are Unggoy, the Jackals are Kig-yar, the Elites are Sangheili, the Brutes are Jiralhanae, the Drones are Yanme, the Hunters are Lekgolo, and the Engineers are Huragok. They're all brought together by belief in the Great Journey.