For me the game was easiest, when I did put both cubes in one corner, which defies the purpose of having two cubes in the first place (:
Oftentimes enemies cannot even hit you, when sitting in a corner, because they cant shoot that way (e.g. 1st & 2nd wave: blue cube in the first corner counterclockwise, red cube in the second corner clockwise (starting counting at top) = win)
Another thing problem to difficulty might be, that waves are totally predefined. Allowing enemies to be of random color might align difficulty more, because then you could not plan ahead.
Unless planning ahead is intended, that is. In that case the difficulty alignment might be better, when adding more waves in strategic positions to force players to move their well placed cubes.
I'd would suggest the forcing of movement and the strategic approach, because it could solve both issues (cube "fortresses" & difficulty alignment). Also there are a lot of browser action games and emphasizing on the strategic aspect of might make this game really stand out.