As for the question, I'd be curious to know what male video game characters people think would best 'represent' males? I'd say if you think about like that, the OP's question becomes a little more silly. This thread is basically about listing female characters who are the least stereotypical or are very empowered. Its an exercise in political correctness.
Okay...I guess there are two definitions. Idealized characters and realistic characters. Idealized men and women tend to be exaggerated representations of how men see themselves and how they want to see women. Realistic however is...well, realistic. Characters that aren't doing much to impress anyone are probably the most realistic.
Realistic "Best Representation"
Male:
Gorman from Majora's Mask, Carpenter's Apprentice in Majora's Mask, James from Silent Hill 2 etc. Real men have a crap ton of depth, they wear facades and when they break they do not always break gracefully. They are good and bad, wrong and right, weak and strong. Each character has a mix of meekness and strength.
Women:
Mary from Silent Hill 2, Anju from Majora's Mask...That's a short list. But you get the idea that they have a lot of depth too. They are weak and frail, they suck at being perfect for their spouse. They wear facades of politeness and kindness but every now and then you see they are definitely not always good people. You also see loyalty and strength along with doubt and fear.
Notice these guys are rarely protagonists...?
Idealistic "Best Representation"
Male:
Perfect and hyper masculine: Kratos, Marcus, Batman etc
Perfect and relatable: Link, Mario, Nathan Drake etc
Female:
Perfect, frail and chaste: Zelda, Peach, Aerith, Ellie etc
Perfect and sexy: Samus, Bayonetta, Lara Croft etc
Just for some parallels...Ancient Rome was really into idealistic figures, but during times of depression and war they started to enjoy drawing old women and men and getting really realistic and emotional with their sculpture. Compare Classic Roman art to late Hellenistic Roman art.