Good system, but
the "primary and secondary weapon" thing is completely pointless. Your weapon set doesn't cooldown while on the other set. There's no real benefit to using the other set. Really makes the game unenjoyable (especially when you get later in the game when you NEED that first set cooling while using the second set).
Also, a sandbox mode would be cool for this (i.e. if you die, you get to try that level again so you keep your upgrades).