This is one of the more inventive games that I've seen on Newgrounds in a while. Despite the need for polish, your natural selection for the minions is very organic and the level of change each generation is fun to follow. I would recommend the following for future iterations:
1) Story: Add some context for the actions of the minion master. The game is fun, but giving him a purpose would take it to the next level.
2) More control over the minions: Being able to give them standing orders (attack, defend, carry, etc) while keeping their spastic movement patterns might be a challenge, but could be fun. These commands would have to be group oriented since I wouldn't want to sub-select minions. Plus, with the ever-changing attributes of the minions, it would force the player to adapt play-strategy as well.