Yea, it's definitely what makes the game a challenge. What I was thinking, is something like, use different keys for them, but while one character is moving, the other can't. Moving both simultaneously would change the dynamics.
Agree with the mouse skip, but I like the feel of the game.
Not sure about individual controls, that may defeat the purpose of the game, but it definitely is irritating switching between them.
Which engine did you build in?
Add levels; start with just 4 to remember.
Add sound control buttons.
Also the game is really big for my screen, I just don't see why it needs to be so big?
That said, I like this type of game. It's well made and simple.
 "Not a Clone Demo"){kind=icon}
 "Dawn of the Dragons"){kind=icon}
 "Rotiart"){kind=icon}
 "Space Mates"){kind=icon}
 "Akarn"){kind=icon}
 "Finna"){kind=icon}
 "Haukr"){kind=icon}
 "HyperBoarder"){kind=icon}
 "Memerize"){kind=icon}
 "Ether War"){kind=icon}
 "Cat And Mouse"){kind=icon}
 "Dojo of Death"){kind=icon}
 "Easy Joe 2"){kind=icon}
 "Effing Worms 2"){kind=icon}
 "William and Sly 2"){kind=icon}
 "BR's Climate Chaos"){kind=icon}
 "The Trader of Stories"){kind=icon}
 "Into Space 2"){kind=icon}
Thanks for playing. I used Stencyl to make it. Yeah, the ship starts out too slow... ;p