If you're talking about skilled protagonists, the ones I can think off the top of my head are
Sharin no Kuni, Himawari no Shoujo (MC is a 'Special High Class Individual)
and its sequel, Yuukyuu no Shounenshoujo
G-senjou no Maou (The MC is the brain of a Yakuza Empire)
9-nine series (MC is not an anti-hero, but is highly capable, especially in the final episode)
Muv-Luv (Extra, Unlimited and Alternative) - MC starts off whiny, weak and insubstantial, but transforms into one of the best protagonists probably of all time
Ayakashibito (MC is an escapee from an internment camp)
Sorcery Jokers (The MC with white hair is a true badass)
There's probably a bunch more, so I'll update this if I remember.