Can Mikumo Megane-kun be considered a shonen anti-hero?
"An antihero or antiheroine is a protagonist who lacks conventional heroic qualities such as idealism, courage, and morality."-Wikipedia

Mikumo definitely does not fit this definition of an anti-hero.  Those would generally be characters such as Deadpool, Punisher, etc from Western Comics.  I feel this is probably the well understood definition.

Apparently (according to TVTropes which I gave into looking up)  a Classic Antihero is plagued by self-doubt and a mediocre fighter. While Mikumo is brave when needed and clever, he clearly fits that (less familiar to me) definition. There are several more sympathetic heroes in Shonen who have uber super powered friends.  In these cases, this definition would call this character (Elizabeth, Lucy, Ussop, Ganta, etc) the Classical Antihero while they have a contrasting Classical Hero (Meliodas, Natsu, Luffy, Shiro, etc).