Hm, "Universe at War: Earth Assault" has three alien factions. Hierarchy, Novus and Masari. There are humans but they're depicted more as an unfortunate victim caught in the middle of a three way war on Earth.
I'll agree with Nelia Hawk: Warhammer 40,000 games could be interesting to the end of a different view of humans. The Imperial Guard is made up of average humans who're depicted as poorly equipped, tank toting, mass deployed fodder against vastly more powerful foes. It's not really different stats though. In a universe of war, humans breed fast enough to have near limitless numbers of reinforcements. Space Marines are super humans with excess organs and heavy armour, better tanks and equipment, etc.
Though, humans in 40k aren't so much different as they are exaggerated. Take traits of humanity and turn them to 11. Xenophobia, paranoia, superstition, warmongering. Game wise, "Dawn of War" 1 and 2, "Warhammer 40,000: Space Marine", "Warhammer 40,000 Epic: Final Liberation". Other than those there's not really that many more.
Hn, "Sid Meier's: Alpha Centauri" is a Civilization type game where you play as one of a number of factions of human colonies on Alpha Centauri. They're split along different ideologies. There is aliens but they're more of a neutral hazard to all, though I believe some of the factions can weaponize them.