I decided to make an all human team, of people who might actually, concievably work together in some way. So no amoral psychopaths like Kratos or Alex Mercer.
Team Leader - Female Commander Shepard (Mass Effect) - A no-brainer really. By far the best example of a leader in videogaming. She knows how to get shit done and kicks all kinds of arse.
Weapons Expert - Rikku (FFX)- A master of mechanics AND magic, able to dismantle even the most dangerous machina in seconds, and then combine any number of items together to create ANY desired effect, Rikku is the ultimate technomage. Even in-game she's the sole reason you're eventually able to upgrade your gear. And she can handle herself in a fight.
Muscle - Dante (DMC 1,3-4) - Not perhaps the most obvious choice, but when you need a guy who can wreck faces and kill a whole bunch of stuff, you can't go wrong with the near unkillable half-demon, physics defying, gunslinging, swordmaster that is Dante. And if you need to fight hordes of demons...
Lone Wolf - Lara Croft (Tomb Raider, any game) - An even less obvious choice than above, but it seems pretty clear when you think about it; Lara has defeated immortal aliens, dragons, the undead, genetic mutants, all manner of mystical entities, dinosaurs and even gods, and she did it all solo. She also brings some specialized knowledge to the team, in the form of knowledge of ancient cultures, languages and the occult.
Stealth Expert - Garrett (Theif) - Another no-brainer, this guy is the ultimate ghost. Where others require teleportation powers or stealth cloaks or all kinds of advanced equipment, Garrett gets by unseen and leaves without a trace purely by skill and the occasional use of a longbow. There is no greater stealth expert.
Jack of All Trades - JC Denton (Deus Ex) - Cybernetically modified with nanites to enhance his skills and installed with a dozen implants to increase his speed and strength, cloak, see through walls, become invulnerable and immune to toxins, breathe underwater AND trained in espionage, diplomacy, various combat disciplines, hacking, medicine and god knows what else, JC is an all-round badass who can find a role in any team.
There, even got a nice 50/50 split on gender roles.