Why do people keep lumping them in with skills? They are really nothing like skills. They seem fairly unrelated too.
Because their BP costs fit in more neatly with skills than they do with Qualities, and because there's a 35 bp hard cap on Qualities. When in doubt -- during character creation -- my gut reaction is always to screw the character as little as possible. Having Martial Arts already suck points from Qualities is one thing I house rule away, and I can't think of any reason to lump maneuvers in there, too (to further eat into the 35).